Working with gene:  NRAS
RASN_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:40:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NRAS.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NRAS.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NRAS.stick_fig.txt NRAS.stick_fig.png

Working with gene:  BRAF
BRAF_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:40:20 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/BRAF.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file BRAF.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/BRAF.stick_fig.txt BRAF.stick_fig.png

Working with gene:  CDKN2A
CD2A1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:40:28 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CDKN2A.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CDKN2A.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CDKN2A.stick_fig.txt CDKN2A.stick_fig.png

Working with gene:  RTL1
RTL1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:40:35 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RTL1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RTL1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RTL1.stick_fig.txt RTL1.stick_fig.png

Working with gene:  EYS
EYS_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:40:42 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/EYS.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file EYS.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/EYS.stick_fig.txt EYS.stick_fig.png

Working with gene:  DNAH6
DYH6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:40:48 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DNAH6.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DNAH6.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DNAH6.stick_fig.txt DNAH6.stick_fig.png

Working with gene:  SPRR3
SPRR3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:40:55 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SPRR3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SPRR3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SPRR3.stick_fig.txt SPRR3.stick_fig.png

Working with gene:  SMR3A
SMR3A_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:41:02 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SMR3A.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SMR3A.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SMR3A.stick_fig.txt SMR3A.stick_fig.png

Working with gene:  CCNE2
CCNE2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:41:09 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CCNE2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CCNE2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CCNE2.stick_fig.txt CCNE2.stick_fig.png

Working with gene:  NOTCH2
NOTC2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:41:16 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NOTCH2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NOTCH2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NOTCH2.stick_fig.txt NOTCH2.stick_fig.png

Working with gene:  PPT2
PPT2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:41:23 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PPT2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PPT2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PPT2.stick_fig.txt PPT2.stick_fig.png

Working with gene:  TAF1A
TAF1A_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:41:30 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TAF1A.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TAF1A.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TAF1A.stick_fig.txt TAF1A.stick_fig.png

Working with gene:  LIPF
LIPG_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:41:36 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LIPF.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LIPF.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LIPF.stick_fig.txt LIPF.stick_fig.png

Working with gene:  ADAM30
ADA30_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:41:43 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ADAM30.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ADAM30.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ADAM30.stick_fig.txt ADAM30.stick_fig.png

Working with gene:  NAP1L4
NP1L4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:41:50 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NAP1L4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NAP1L4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NAP1L4.stick_fig.txt NAP1L4.stick_fig.png

Working with gene:  DEFB115
DB115_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:41:58 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DEFB115.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DEFB115.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DEFB115.stick_fig.txt DEFB115.stick_fig.png

Working with gene:  PTEN
PTEN_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:42:05 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PTEN.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PTEN.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PTEN.stick_fig.txt PTEN.stick_fig.png

Working with gene:  INTS8
INT8_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:42:13 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/INTS8.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file INTS8.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/INTS8.stick_fig.txt INTS8.stick_fig.png

Working with gene:  TBC1D3
TBC3A_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:42:20 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TBC1D3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TBC1D3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TBC1D3.stick_fig.txt TBC1D3.stick_fig.png

Working with gene:  TP53
P53_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:42:27 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TP53.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TP53.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TP53.stick_fig.txt TP53.stick_fig.png

Working with gene:  DISP1
DISP1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:42:35 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DISP1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DISP1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DISP1.stick_fig.txt DISP1.stick_fig.png

Working with gene:  STK31
STK31_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:42:42 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/STK31.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file STK31.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/STK31.stick_fig.txt STK31.stick_fig.png

Working with gene:  PRC1
PRC1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:42:50 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PRC1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PRC1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PRC1.stick_fig.txt PRC1.stick_fig.png

Working with gene:  CDC123
CD123_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:42:57 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CDC123.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CDC123.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CDC123.stick_fig.txt CDC123.stick_fig.png

Working with gene:  IVL
INVO_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:43:03 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IVL.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file IVL.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IVL.stick_fig.txt IVL.stick_fig.png

Working with gene:  DPY19L4
D19L4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:43:09 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DPY19L4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DPY19L4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DPY19L4.stick_fig.txt DPY19L4.stick_fig.png

Working with gene:  CLCC1
CLCC1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:43:16 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CLCC1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CLCC1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CLCC1.stick_fig.txt CLCC1.stick_fig.png

Working with gene:  ZNF860
ZN860_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:43:23 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZNF860.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ZNF860.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZNF860.stick_fig.txt ZNF860.stick_fig.png

Working with gene:  IDH1
IDHC_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:43:30 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IDH1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file IDH1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IDH1.stick_fig.txt IDH1.stick_fig.png

Working with gene:  RPTN
RPTN_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:43:37 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RPTN.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RPTN.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RPTN.stick_fig.txt RPTN.stick_fig.png

Working with gene:  PPP6C
PPP6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:43:44 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PPP6C.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PPP6C.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PPP6C.stick_fig.txt PPP6C.stick_fig.png

Working with gene:  CECR6
CECR6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:43:52 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CECR6.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CECR6.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CECR6.stick_fig.txt CECR6.stick_fig.png

Working with gene:  THADA
THADA_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:43:59 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/THADA.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file THADA.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/THADA.stick_fig.txt THADA.stick_fig.png

Working with gene:  PIK3CB
PK3CB_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:44:07 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PIK3CB.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PIK3CB.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PIK3CB.stick_fig.txt PIK3CB.stick_fig.png

Working with gene:  ADAM21
ADA21_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:44:14 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ADAM21.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ADAM21.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ADAM21.stick_fig.txt ADAM21.stick_fig.png

Working with gene:  TCHHL1
TCHL1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:44:21 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TCHHL1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TCHHL1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TCHHL1.stick_fig.txt TCHHL1.stick_fig.png

Working with gene:  PRB1
PRP1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:44:29 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PRB1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PRB1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PRB1.stick_fig.txt PRB1.stick_fig.png

Working with gene:  ARID2
ARID2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:44:37 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ARID2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ARID2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ARID2.stick_fig.txt ARID2.stick_fig.png

Working with gene:  EIF2AK3
E2AK3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:44:44 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/EIF2AK3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file EIF2AK3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/EIF2AK3.stick_fig.txt EIF2AK3.stick_fig.png

Working with gene:  F2RL1
PAR2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:44:50 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/F2RL1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file F2RL1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/F2RL1.stick_fig.txt F2RL1.stick_fig.png

Working with gene:  LIPH
LIPH_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:44:57 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LIPH.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LIPH.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LIPH.stick_fig.txt LIPH.stick_fig.png

Working with gene:  PROL1
PROL1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:45:05 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PROL1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PROL1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PROL1.stick_fig.txt PROL1.stick_fig.png

Working with gene:  NBPF7
NBPF7_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:45:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NBPF7.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NBPF7.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NBPF7.stick_fig.txt NBPF7.stick_fig.png

Working with gene:  DSG3
DSG3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:45:19 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DSG3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DSG3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DSG3.stick_fig.txt DSG3.stick_fig.png

Working with gene:  PHGDH
SERA_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:45:26 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PHGDH.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PHGDH.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PHGDH.stick_fig.txt PHGDH.stick_fig.png

Working with gene:  FMNL2
FMNL2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:45:33 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FMNL2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FMNL2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FMNL2.stick_fig.txt FMNL2.stick_fig.png

Working with gene:  BCLAF1
BCLF1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:45:42 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/BCLAF1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file BCLAF1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/BCLAF1.stick_fig.txt BCLAF1.stick_fig.png

Working with gene:  NMS
NMS_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:45:49 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NMS.stick_fig.txt
{??? Error using ==> mutfig at 150
Definition must include exactly one "protein" record
} 

FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NMS.stick_fig.txt NMS.stick_fig.png
Traceback (most recent call last):
  File "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/run_matlab.py", line 98, in <module>
    runMatlab()
  File "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/run_matlab.py", line 71, in runMatlab
    subprocess.check_call(matlabCommand)
  File "/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.6.6/lib/python2.6/subprocess.py", line 488, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig', '/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NMS.stick_fig.txt', 'NMS.stick_fig.png']' returned non-zero exit status 255

Working with gene:  FCHSD2
FCSD2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:45:53 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FCHSD2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FCHSD2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FCHSD2.stick_fig.txt FCHSD2.stick_fig.png

Working with gene:  EIF2B1
EI2BA_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:46:00 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/EIF2B1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file EIF2B1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/EIF2B1.stick_fig.txt EIF2B1.stick_fig.png

Working with gene:  LALBA
LALBA_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:46:08 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LALBA.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LALBA.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LALBA.stick_fig.txt LALBA.stick_fig.png

Working with gene:  NBEAL1
NBEL1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:46:15 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NBEAL1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NBEAL1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NBEAL1.stick_fig.txt NBEAL1.stick_fig.png

Working with gene:  DNAH12
DYH12_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:46:22 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DNAH12.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DNAH12.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DNAH12.stick_fig.txt DNAH12.stick_fig.png

Working with gene:  POTED
POTED_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:46:29 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/POTED.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file POTED.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/POTED.stick_fig.txt POTED.stick_fig.png

Working with gene:  PALMD
PALMD_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:46:36 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PALMD.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PALMD.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PALMD.stick_fig.txt PALMD.stick_fig.png

Working with gene:  STK19
STK19_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:46:43 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/STK19.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file STK19.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/STK19.stick_fig.txt STK19.stick_fig.png

Working with gene:  PRB4
PRB4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:46:49 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PRB4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PRB4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PRB4.stick_fig.txt PRB4.stick_fig.png

Working with gene:  BLM
BLM_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:46:56 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/BLM.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file BLM.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/BLM.stick_fig.txt BLM.stick_fig.png

Working with gene:  SPRR2G
SPR2G_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:47:03 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SPRR2G.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SPRR2G.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SPRR2G.stick_fig.txt SPRR2G.stick_fig.png

Working with gene:  XKR5
XKR5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:47:09 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/XKR5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file XKR5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/XKR5.stick_fig.txt XKR5.stick_fig.png

Working with gene:  PARM1
PARM1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:47:16 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PARM1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PARM1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PARM1.stick_fig.txt PARM1.stick_fig.png

Working with gene:  GFRAL
GFRAL_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:47:22 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GFRAL.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GFRAL.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GFRAL.stick_fig.txt GFRAL.stick_fig.png

Working with gene:  CEP70
CEP70_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:47:30 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CEP70.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CEP70.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CEP70.stick_fig.txt CEP70.stick_fig.png

Working with gene:  SYCP1
SYCP1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:47:37 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SYCP1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SYCP1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SYCP1.stick_fig.txt SYCP1.stick_fig.png

Working with gene:  TXNDC3
TXND3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:47:44 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TXNDC3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TXNDC3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TXNDC3.stick_fig.txt TXNDC3.stick_fig.png

Working with gene:  SLC9A11
S9A11_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:47:51 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC9A11.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SLC9A11.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC9A11.stick_fig.txt SLC9A11.stick_fig.png

Working with gene:  COPG2
COPG2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:47:59 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COPG2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file COPG2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COPG2.stick_fig.txt COPG2.stick_fig.png

Working with gene:  OR5H14
O5H14_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:48:06 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR5H14.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR5H14.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR5H14.stick_fig.txt OR5H14.stick_fig.png

Working with gene:  NSUN7
Gene NSUN7 does not have swiss prot accession ID in MAF file. Skipping gene... 
Working with gene:  COL4A4
CO4A4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:48:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL4A4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file COL4A4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL4A4.stick_fig.txt COL4A4.stick_fig.png

Working with gene:  SAMD9L
SAM9L_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:48:19 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SAMD9L.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SAMD9L.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SAMD9L.stick_fig.txt SAMD9L.stick_fig.png

Working with gene:  TAX1BP1
TAXB1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:48:26 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TAX1BP1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TAX1BP1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TAX1BP1.stick_fig.txt TAX1BP1.stick_fig.png

Working with gene:  DDX3X
DDX3X_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:48:33 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DDX3X.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DDX3X.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DDX3X.stick_fig.txt DDX3X.stick_fig.png

Working with gene:  POF1B
POF1B_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:48:40 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/POF1B.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file POF1B.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/POF1B.stick_fig.txt POF1B.stick_fig.png

Working with gene:  GIMAP7
GIMA7_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:48:47 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GIMAP7.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GIMAP7.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GIMAP7.stick_fig.txt GIMAP7.stick_fig.png

Working with gene:  CLEC4E
CLC4E_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:48:54 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CLEC4E.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CLEC4E.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CLEC4E.stick_fig.txt CLEC4E.stick_fig.png

Working with gene:  OR5H2
OR5H2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:49:00 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR5H2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR5H2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR5H2.stick_fig.txt OR5H2.stick_fig.png

Working with gene:  PRB2
Gene PRB2 does not have swiss prot accession ID in MAF file. Skipping gene... 
Working with gene:  CXorf21
CX021_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:49:07 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CXorf21.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CXorf21.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CXorf21.stick_fig.txt CXorf21.stick_fig.png

Working with gene:  C12orf43
CL043_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:49:15 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C12orf43.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file C12orf43.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C12orf43.stick_fig.txt C12orf43.stick_fig.png

Working with gene:  COL4A5
CO4A5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:49:21 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL4A5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file COL4A5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL4A5.stick_fig.txt COL4A5.stick_fig.png

Working with gene:  RPGRIP1L
FTM_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:49:28 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RPGRIP1L.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RPGRIP1L.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RPGRIP1L.stick_fig.txt RPGRIP1L.stick_fig.png

Working with gene:  MORC1
MORC1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:49:35 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MORC1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MORC1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MORC1.stick_fig.txt MORC1.stick_fig.png

Working with gene:  CYP3A43
CP343_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:49:43 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CYP3A43.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CYP3A43.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CYP3A43.stick_fig.txt CYP3A43.stick_fig.png

Working with gene:  ZFX
ZFX_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:49:51 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZFX.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ZFX.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZFX.stick_fig.txt ZFX.stick_fig.png

Working with gene:  DEFB118
DB118_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:49:58 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DEFB118.stick_fig.txt
{??? Error using ==> mutfig at 150
Definition must include exactly one "protein" record
} 

FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DEFB118.stick_fig.txt DEFB118.stick_fig.png
Traceback (most recent call last):
  File "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/run_matlab.py", line 98, in <module>
    runMatlab()
  File "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/run_matlab.py", line 71, in runMatlab
    subprocess.check_call(matlabCommand)
  File "/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.6.6/lib/python2.6/subprocess.py", line 488, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig', '/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DEFB118.stick_fig.txt', 'DEFB118.stick_fig.png']' returned non-zero exit status 255

Working with gene:  CLGN
CLGN_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:50:02 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CLGN.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CLGN.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CLGN.stick_fig.txt CLGN.stick_fig.png

Working with gene:  NF1
NF1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:50:09 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NF1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NF1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NF1.stick_fig.txt NF1.stick_fig.png

Working with gene:  IL1R1
IL1R1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:50:22 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IL1R1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file IL1R1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IL1R1.stick_fig.txt IL1R1.stick_fig.png

Working with gene:  TSGA14
CEP41_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:50:29 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TSGA14.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TSGA14.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TSGA14.stick_fig.txt TSGA14.stick_fig.png

Working with gene:  UGT2A3
UD2A3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:50:35 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/UGT2A3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file UGT2A3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/UGT2A3.stick_fig.txt UGT2A3.stick_fig.png

Working with gene:  SV2B
SV2B_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:50:42 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SV2B.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SV2B.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SV2B.stick_fig.txt SV2B.stick_fig.png

Working with gene:  RIMBP3
Gene RIMBP3 does not have swiss prot accession ID in MAF file. Skipping gene... 
Working with gene:  RGS22
RGS22_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:50:50 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RGS22.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RGS22.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RGS22.stick_fig.txt RGS22.stick_fig.png

Working with gene:  CYP3A4
CP3A4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:50:58 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CYP3A4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CYP3A4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CYP3A4.stick_fig.txt CYP3A4.stick_fig.png

Working with gene:  RAC1
RAC1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:51:05 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RAC1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RAC1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RAC1.stick_fig.txt RAC1.stick_fig.png

Working with gene:  RNF17
RNF17_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:51:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RNF17.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RNF17.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RNF17.stick_fig.txt RNF17.stick_fig.png

Working with gene:  LRP6
LRP6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:51:20 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LRP6.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LRP6.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LRP6.stick_fig.txt LRP6.stick_fig.png

Working with gene:  GABRG1
GBRG1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:51:27 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GABRG1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GABRG1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GABRG1.stick_fig.txt GABRG1.stick_fig.png

Working with gene:  FRG2B
FRG2B_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:51:36 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FRG2B.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FRG2B.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FRG2B.stick_fig.txt FRG2B.stick_fig.png

Working with gene:  SDR16C5
RDHE2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:51:43 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SDR16C5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SDR16C5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SDR16C5.stick_fig.txt SDR16C5.stick_fig.png

Working with gene:  ART3
NAR3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:51:50 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ART3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ART3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ART3.stick_fig.txt ART3.stick_fig.png

Working with gene:  OR4Q3
OR4Q3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:51:58 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR4Q3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR4Q3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR4Q3.stick_fig.txt OR4Q3.stick_fig.png

Working with gene:  UPF2
RENT2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:52:05 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/UPF2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file UPF2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/UPF2.stick_fig.txt UPF2.stick_fig.png

Working with gene:  SERPINB4
SPB4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:52:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SERPINB4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SERPINB4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SERPINB4.stick_fig.txt SERPINB4.stick_fig.png

Working with gene:  SEMG1
SEMG1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:52:19 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SEMG1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SEMG1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SEMG1.stick_fig.txt SEMG1.stick_fig.png

Working with gene:  ADH1B
ADH1B_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:52:26 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ADH1B.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ADH1B.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ADH1B.stick_fig.txt ADH1B.stick_fig.png

Working with gene:  NAIP
BIRC1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:52:33 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NAIP.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NAIP.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NAIP.stick_fig.txt NAIP.stick_fig.png

Working with gene:  SLC5A3
SC5A3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:52:40 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC5A3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SLC5A3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC5A3.stick_fig.txt SLC5A3.stick_fig.png

Working with gene:  GLYAT
GLYAT_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:52:47 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GLYAT.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GLYAT.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GLYAT.stick_fig.txt GLYAT.stick_fig.png

Working with gene:  IL33
IL33_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:52:54 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IL33.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file IL33.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IL33.stick_fig.txt IL33.stick_fig.png

Working with gene:  BIN2
BIN2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:53:01 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/BIN2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file BIN2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/BIN2.stick_fig.txt BIN2.stick_fig.png

Working with gene:  CD2
CD2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:53:08 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CD2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CD2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CD2.stick_fig.txt CD2.stick_fig.png

Working with gene:  USP29
UBP29_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:53:15 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/USP29.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file USP29.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/USP29.stick_fig.txt USP29.stick_fig.png

Working with gene:  GLYATL2
GLYL2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:53:23 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GLYATL2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GLYATL2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GLYATL2.stick_fig.txt GLYATL2.stick_fig.png

Working with gene:  BAT3
BAG6_HUMAN
Problem with retrieving features for gene: swiss prot ID likely not found in features database.
Working with gene:  HSD11B1
DHI1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:53:30 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/HSD11B1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file HSD11B1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/HSD11B1.stick_fig.txt HSD11B1.stick_fig.png

Working with gene:  COL21A1
COLA1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:53:37 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL21A1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file COL21A1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL21A1.stick_fig.txt COL21A1.stick_fig.png

Working with gene:  PASD1
PASD1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:53:45 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PASD1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PASD1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PASD1.stick_fig.txt PASD1.stick_fig.png

Working with gene:  PPP1R3A
PPR3A_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:53:52 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PPP1R3A.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PPP1R3A.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PPP1R3A.stick_fig.txt PPP1R3A.stick_fig.png

Working with gene:  PPM1B
PPM1B_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:53:59 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PPM1B.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PPM1B.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PPM1B.stick_fig.txt PPM1B.stick_fig.png

Working with gene:  OR2B3
Gene OR2B3 does not have swiss prot accession ID in MAF file. Skipping gene... 
Working with gene:  APC2
APC2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:54:05 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/APC2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file APC2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/APC2.stick_fig.txt APC2.stick_fig.png

Working with gene:  MECOM
EVI1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:54:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MECOM.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MECOM.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MECOM.stick_fig.txt MECOM.stick_fig.png

Working with gene:  SLC9A10
S9A10_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:54:19 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC9A10.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SLC9A10.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC9A10.stick_fig.txt SLC9A10.stick_fig.png

Working with gene:  KRTAP15-1
KR151_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:54:26 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/KRTAP15-1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file KRTAP15-1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/KRTAP15-1.stick_fig.txt KRTAP15-1.stick_fig.png

Working with gene:  YSK4
YSK4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:54:33 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/YSK4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file YSK4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/YSK4.stick_fig.txt YSK4.stick_fig.png

Working with gene:  COL17A1
COHA1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:54:41 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL17A1.stick_fig.txt
{??? Error using ==> rectangle
Values must be finite and non-NaN

Error in ==> mutfig at 228


} 
MATLAB:hg:set_chck:Matrix_to_matlabRect_set_check_fcn:ExpectedFiniteNonNaN
{Warning: 1 visible figure(s) exist at MCR termination.
} 
{If your application has terminated unexpectedly, please note that 
 applications generated by the MATLAB Compiler terminate when there are no 
 visible figure windows. See the documentation for WaitForFiguresToDie and
 WAITFORCALLBACKS for more information.
} 
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL17A1.stick_fig.txt COL17A1.stick_fig.png
Traceback (most recent call last):
  File "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/run_matlab.py", line 98, in <module>
    runMatlab()
  File "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/run_matlab.py", line 71, in runMatlab
    subprocess.check_call(matlabCommand)
  File "/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.6.6/lib/python2.6/subprocess.py", line 488, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig', '/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL17A1.stick_fig.txt', 'COL17A1.stick_fig.png']' returned non-zero exit status 255

Working with gene:  CCDC68
CCD68_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:54:45 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CCDC68.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CCDC68.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CCDC68.stick_fig.txt CCDC68.stick_fig.png

Working with gene:  NPY1R
NPY1R_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:54:52 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NPY1R.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NPY1R.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NPY1R.stick_fig.txt NPY1R.stick_fig.png

Working with gene:  IL21
IL21_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:54:59 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IL21.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file IL21.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IL21.stick_fig.txt IL21.stick_fig.png

Working with gene:  FETUB
FETUB_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:55:06 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FETUB.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FETUB.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FETUB.stick_fig.txt FETUB.stick_fig.png

Working with gene:  MYOCD
MYCD_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:55:13 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MYOCD.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MYOCD.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MYOCD.stick_fig.txt MYOCD.stick_fig.png

Working with gene:  TLR2
TLR2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:55:20 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TLR2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TLR2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TLR2.stick_fig.txt TLR2.stick_fig.png

Working with gene:  SLC38A4
S38A4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:55:26 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC38A4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SLC38A4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC38A4.stick_fig.txt SLC38A4.stick_fig.png

Working with gene:  IDO2
I23O2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:55:34 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IDO2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file IDO2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IDO2.stick_fig.txt IDO2.stick_fig.png

Working with gene:  HDC
DCHS_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:55:40 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/HDC.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file HDC.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/HDC.stick_fig.txt HDC.stick_fig.png

Working with gene:  MUC7
MUC7_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:55:47 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MUC7.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MUC7.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MUC7.stick_fig.txt MUC7.stick_fig.png

Working with gene:  AMHR2
AMHR2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:55:57 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/AMHR2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file AMHR2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/AMHR2.stick_fig.txt AMHR2.stick_fig.png

Working with gene:  TRAT1
TRAT1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:56:03 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TRAT1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TRAT1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TRAT1.stick_fig.txt TRAT1.stick_fig.png

Working with gene:  ADAM7
ADAM7_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:56:10 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ADAM7.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ADAM7.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ADAM7.stick_fig.txt ADAM7.stick_fig.png

Working with gene:  RAG2
RAG2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:56:18 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RAG2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RAG2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RAG2.stick_fig.txt RAG2.stick_fig.png

Working with gene:  SLC16A9
MOT9_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:56:24 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC16A9.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SLC16A9.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC16A9.stick_fig.txt SLC16A9.stick_fig.png

Working with gene:  C1orf150
CA150_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:56:31 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C1orf150.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file C1orf150.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C1orf150.stick_fig.txt C1orf150.stick_fig.png

Working with gene:  SP140L
LY10L_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:56:38 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SP140L.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SP140L.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SP140L.stick_fig.txt SP140L.stick_fig.png

Working with gene:  SPANXN3
SPXN3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:56:44 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SPANXN3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SPANXN3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SPANXN3.stick_fig.txt SPANXN3.stick_fig.png

Working with gene:  NDST4
NDST4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:56:51 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NDST4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NDST4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NDST4.stick_fig.txt NDST4.stick_fig.png

Working with gene:  LRPPRC
LPPRC_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:56:58 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LRPPRC.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LRPPRC.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LRPPRC.stick_fig.txt LRPPRC.stick_fig.png

Working with gene:  ANO4
ANO4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:57:05 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ANO4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ANO4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ANO4.stick_fig.txt ANO4.stick_fig.png

Working with gene:  GPR174
GP174_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:57:13 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GPR174.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GPR174.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GPR174.stick_fig.txt GPR174.stick_fig.png

Working with gene:  MAN2A2
MA2A2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:57:19 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MAN2A2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MAN2A2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MAN2A2.stick_fig.txt MAN2A2.stick_fig.png

Working with gene:  CCDC54
CCD54_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:57:26 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CCDC54.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CCDC54.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CCDC54.stick_fig.txt CCDC54.stick_fig.png

Working with gene:  WFDC8
WFDC8_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:57:32 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/WFDC8.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file WFDC8.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/WFDC8.stick_fig.txt WFDC8.stick_fig.png

Working with gene:  EYA1
EYA1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:57:39 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/EYA1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file EYA1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/EYA1.stick_fig.txt EYA1.stick_fig.png

Working with gene:  MAP2K1
MP2K1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:57:46 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MAP2K1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MAP2K1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MAP2K1.stick_fig.txt MAP2K1.stick_fig.png

Working with gene:  L1TD1
LITD1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:57:54 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/L1TD1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file L1TD1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/L1TD1.stick_fig.txt L1TD1.stick_fig.png

Working with gene:  LOC649330
B7ZW38_HUMAN
Problem with retrieving features for gene: swiss prot ID likely not found in features database.
Working with gene:  SAMD12
SAM12_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:58:01 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SAMD12.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SAMD12.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SAMD12.stick_fig.txt SAMD12.stick_fig.png

Working with gene:  GRXCR2
GRCR2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:58:08 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GRXCR2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GRXCR2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GRXCR2.stick_fig.txt GRXCR2.stick_fig.png

Working with gene:  ADH1C
ADH1G_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:58:15 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ADH1C.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ADH1C.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ADH1C.stick_fig.txt ADH1C.stick_fig.png

Working with gene:  CYLC1
CYLC1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:58:23 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CYLC1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CYLC1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CYLC1.stick_fig.txt CYLC1.stick_fig.png

Working with gene:  ZSWIM2
ZSWM2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:58:30 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZSWIM2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ZSWIM2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZSWIM2.stick_fig.txt ZSWIM2.stick_fig.png

Working with gene:  OR4C11
OR4CB_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:58:38 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR4C11.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR4C11.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR4C11.stick_fig.txt OR4C11.stick_fig.png

Working with gene:  GPRIN2
GRIN2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:58:44 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GPRIN2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GPRIN2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GPRIN2.stick_fig.txt GPRIN2.stick_fig.png

Working with gene:  IDE
IDE_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:58:51 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IDE.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file IDE.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IDE.stick_fig.txt IDE.stick_fig.png

Working with gene:  MUC17
MUC17_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:58:58 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MUC17.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MUC17.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MUC17.stick_fig.txt MUC17.stick_fig.png

Working with gene:  DSCR6
DSCR6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:59:07 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DSCR6.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DSCR6.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DSCR6.stick_fig.txt DSCR6.stick_fig.png

Working with gene:  CAPSL
CAPSL_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:59:14 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CAPSL.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CAPSL.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CAPSL.stick_fig.txt CAPSL.stick_fig.png

Working with gene:  LIPI
LIPI_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:59:21 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LIPI.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LIPI.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LIPI.stick_fig.txt LIPI.stick_fig.png

Working with gene:  C15orf55
NUT_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:59:27 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C15orf55.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file C15orf55.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C15orf55.stick_fig.txt C15orf55.stick_fig.png

Working with gene:  MAGEA11
MAGAB_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:59:36 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MAGEA11.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MAGEA11.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MAGEA11.stick_fig.txt MAGEA11.stick_fig.png

Working with gene:  IL32
IL32_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:59:44 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IL32.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file IL32.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/IL32.stick_fig.txt IL32.stick_fig.png

Working with gene:  COL8A1
CO8A1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:59:53 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL8A1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file COL8A1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL8A1.stick_fig.txt COL8A1.stick_fig.png

Working with gene:  UGT2B10
UDB10_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 00:59:59 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/UGT2B10.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file UGT2B10.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/UGT2B10.stick_fig.txt UGT2B10.stick_fig.png

Working with gene:  EMB
EMB_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:00:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/EMB.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file EMB.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/EMB.stick_fig.txt EMB.stick_fig.png

Working with gene:  PTPN22
PTN22_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:00:19 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PTPN22.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PTPN22.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PTPN22.stick_fig.txt PTPN22.stick_fig.png

Working with gene:  DSC3
DSC3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:00:26 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DSC3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DSC3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DSC3.stick_fig.txt DSC3.stick_fig.png

Working with gene:  CCDC73
CCD73_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:00:33 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CCDC73.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CCDC73.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CCDC73.stick_fig.txt CCDC73.stick_fig.png

Working with gene:  ZNF479
ZN479_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:00:41 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZNF479.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ZNF479.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZNF479.stick_fig.txt ZNF479.stick_fig.png

Working with gene:  C10orf81
CJ081_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:00:48 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C10orf81.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file C10orf81.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C10orf81.stick_fig.txt C10orf81.stick_fig.png

Working with gene:  CADM2
CADM2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:00:55 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CADM2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CADM2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CADM2.stick_fig.txt CADM2.stick_fig.png

Working with gene:  UGT2B28
UDB28_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:01:02 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/UGT2B28.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file UGT2B28.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/UGT2B28.stick_fig.txt UGT2B28.stick_fig.png

Working with gene:  GBA3
GBA3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:01:10 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GBA3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GBA3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GBA3.stick_fig.txt GBA3.stick_fig.png

Working with gene:  WDR47
WDR47_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:01:17 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/WDR47.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file WDR47.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/WDR47.stick_fig.txt WDR47.stick_fig.png

Working with gene:  COL4A3
CO4A3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:01:25 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL4A3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file COL4A3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL4A3.stick_fig.txt COL4A3.stick_fig.png

Working with gene:  LRRIQ3
LRIQ3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:01:34 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LRRIQ3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LRRIQ3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LRRIQ3.stick_fig.txt LRRIQ3.stick_fig.png

Working with gene:  CFHR2
FHR2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:01:42 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CFHR2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CFHR2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CFHR2.stick_fig.txt CFHR2.stick_fig.png

Working with gene:  STXBP5L
STB5L_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:01:48 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/STXBP5L.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file STXBP5L.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/STXBP5L.stick_fig.txt STXBP5L.stick_fig.png

Working with gene:  CFH
CFAH_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:01:56 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CFH.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CFH.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CFH.stick_fig.txt CFH.stick_fig.png

Working with gene:  ZNF883
ZN883_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:02:04 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZNF883.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ZNF883.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZNF883.stick_fig.txt ZNF883.stick_fig.png

Working with gene:  C14orf39
Q08AQ4_HUMAN
Problem with retrieving features for gene: swiss prot ID likely not found in features database.
Working with gene:  FUT9
FUT9_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:02:10 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FUT9.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FUT9.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FUT9.stick_fig.txt FUT9.stick_fig.png

Working with gene:  OR4F6
OR4F6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:02:17 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR4F6.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR4F6.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR4F6.stick_fig.txt OR4F6.stick_fig.png

Working with gene:  GK2
GLPK2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:02:23 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GK2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GK2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/GK2.stick_fig.txt GK2.stick_fig.png

Working with gene:  TDRD5
TDRD5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:02:31 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TDRD5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TDRD5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TDRD5.stick_fig.txt TDRD5.stick_fig.png

Working with gene:  SYCE1
SYCE1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:02:39 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SYCE1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SYCE1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SYCE1.stick_fig.txt SYCE1.stick_fig.png

Working with gene:  C1orf168
CA168_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:02:46 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C1orf168.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file C1orf168.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C1orf168.stick_fig.txt C1orf168.stick_fig.png

Working with gene:  ZEB1
ZEB1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:02:53 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZEB1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ZEB1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZEB1.stick_fig.txt ZEB1.stick_fig.png

Working with gene:  COL5A3
CO5A3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:03:00 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL5A3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file COL5A3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL5A3.stick_fig.txt COL5A3.stick_fig.png

Working with gene:  MARK1
MARK1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:03:09 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MARK1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MARK1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MARK1.stick_fig.txt MARK1.stick_fig.png

Working with gene:  MUM1L1
MUML1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:03:16 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MUM1L1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MUM1L1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MUM1L1.stick_fig.txt MUM1L1.stick_fig.png

Working with gene:  NCOA6
NCOA6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:03:24 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NCOA6.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NCOA6.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/NCOA6.stick_fig.txt NCOA6.stick_fig.png

Working with gene:  COL4A1
CO4A1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:03:31 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL4A1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file COL4A1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/COL4A1.stick_fig.txt COL4A1.stick_fig.png

Working with gene:  FLG2
FILA2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:03:38 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FLG2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FLG2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FLG2.stick_fig.txt FLG2.stick_fig.png

Working with gene:  TAAR2
TAAR2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:03:46 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TAAR2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TAAR2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/TAAR2.stick_fig.txt TAAR2.stick_fig.png

Working with gene:  DPYD
DPYD_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:03:53 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DPYD.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DPYD.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/DPYD.stick_fig.txt DPYD.stick_fig.png

Working with gene:  SLC17A4
S17A4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:04:01 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC17A4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SLC17A4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC17A4.stick_fig.txt SLC17A4.stick_fig.png

Working with gene:  ESRP1
ESRP1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:04:07 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ESRP1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ESRP1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ESRP1.stick_fig.txt ESRP1.stick_fig.png

Working with gene:  OR4A15
O4A15_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:04:14 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR4A15.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR4A15.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR4A15.stick_fig.txt OR4A15.stick_fig.png

Working with gene:  SLC15A2
S15A2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:04:21 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC15A2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SLC15A2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC15A2.stick_fig.txt SLC15A2.stick_fig.png

Working with gene:  C12orf54
CL054_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:04:28 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C12orf54.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file C12orf54.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/C12orf54.stick_fig.txt C12orf54.stick_fig.png

Working with gene:  MIA2
MIA2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:04:35 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MIA2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MIA2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/MIA2.stick_fig.txt MIA2.stick_fig.png

Working with gene:  IL1F8
IL36B_HUMAN
Problem with retrieving features for gene: swiss prot ID likely not found in features database.
Working with gene:  FASLG
TNFL6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:04:44 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FASLG.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FASLG.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FASLG.stick_fig.txt FASLG.stick_fig.png

Working with gene:  CHGB
SCG1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:04:52 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CHGB.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CHGB.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CHGB.stick_fig.txt CHGB.stick_fig.png

Working with gene:  PDE1A
PDE1A_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:05:00 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PDE1A.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PDE1A.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/PDE1A.stick_fig.txt PDE1A.stick_fig.png

Working with gene:  SLC2A12
GTR12_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:05:08 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC2A12.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SLC2A12.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SLC2A12.stick_fig.txt SLC2A12.stick_fig.png

Working with gene:  OR2B2
OR2B2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:05:15 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR2B2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR2B2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/OR2B2.stick_fig.txt OR2B2.stick_fig.png

Working with gene:  ENAM
ENAM_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:05:21 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ENAM.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ENAM.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ENAM.stick_fig.txt ENAM.stick_fig.png

Working with gene:  FRMD7
FRMD7_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:05:29 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FRMD7.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FRMD7.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/FRMD7.stick_fig.txt FRMD7.stick_fig.png

Working with gene:  LCE1B
LCE1B_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:05:36 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LCE1B.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LCE1B.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/LCE1B.stick_fig.txt LCE1B.stick_fig.png

Working with gene:  UGT2B4
UD2B4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:05:43 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/UGT2B4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file UGT2B4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/UGT2B4.stick_fig.txt UGT2B4.stick_fig.png

Working with gene:  CD300A
CLM8_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:05:50 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CD300A.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CD300A.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/CD300A.stick_fig.txt CD300A.stick_fig.png

Working with gene:  ISX
ISX_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:05:58 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ISX.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ISX.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ISX.stick_fig.txt ISX.stick_fig.png

Working with gene:  ZBBX
ZBBX_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:06:06 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZBBX.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ZBBX.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ZBBX.stick_fig.txt ZBBX.stick_fig.png

Working with gene:  ROS1
ROS_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:06:14 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ROS1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ROS1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/ROS1.stick_fig.txt ROS1.stick_fig.png

Working with gene:  SAGE1
SAGE1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:06:22 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SAGE1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SAGE1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SAGE1.stick_fig.txt SAGE1.stick_fig.png

Working with gene:  SAMD7
SAMD7_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:06:30 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SAMD7.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SAMD7.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/SAMD7.stick_fig.txt SAMD7.stick_fig.png

Working with gene:  MORF4
Gene MORF4 does not have swiss prot accession ID in MAF file. Skipping gene... 
Working with gene:  RB1
RB_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:06:39 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 18552
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RB1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RB1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/286996/RB1.stick_fig.txt RB1.stick_fig.png

