Working with gene:  NF2
MERL_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


Thu Jan 10 12:29:02 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/NF2.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 NF2.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/284701
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/284701/NF2.stick_fig.txt NF2.stick_fig.png

Working with gene:  KDM6A
KDM6A_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


Thu Jan 10 12:29:17 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/KDM6A.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 KDM6A.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/284701
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/284701/KDM6A.stick_fig.txt KDM6A.stick_fig.png

Working with gene:  PCF11
PCF11_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


Thu Jan 10 12:29:24 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/PCF11.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 PCF11.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/284701
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/284701/PCF11.stick_fig.txt PCF11.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


Thu Jan 10 12:29:30 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/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/284701
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/284701/IL32.stick_fig.txt IL32.stick_fig.png

Working with gene:  STAG2
STAG2_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


Thu Jan 10 12:29:36 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/STAG2.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 STAG2.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/284701
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/284701/STAG2.stick_fig.txt STAG2.stick_fig.png

Working with gene:  MET
MET_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


Thu Jan 10 12:29:42 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/MET.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 MET.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/284701
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/284701/MET.stick_fig.txt MET.stick_fig.png

Working with gene:  SETD2
SETD2_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


Thu Jan 10 12:29:49 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/SETD2.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 SETD2.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/284701
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/284701/SETD2.stick_fig.txt SETD2.stick_fig.png

Working with gene:  FGFR3
FGFR3_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


Thu Jan 10 12:29:55 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/FGFR3.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 FGFR3.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/284701
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/284701/FGFR3.stick_fig.txt FGFR3.stick_fig.png

Working with gene:  FLJ46321
F75D1_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


Thu Jan 10 12:30:02 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/FLJ46321.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 FLJ46321.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/284701
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/284701/FLJ46321.stick_fig.txt FLJ46321.stick_fig.png

Working with gene:  SRCAP
SRCAP_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


Thu Jan 10 12:30:08 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/SRCAP.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 SRCAP.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/284701
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/284701/SRCAP.stick_fig.txt SRCAP.stick_fig.png

Working with gene:  SRRM2
SRRM2_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


Thu Jan 10 12:30:14 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/SRRM2.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 SRRM2.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/284701
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/284701/SRRM2.stick_fig.txt SRRM2.stick_fig.png

Working with gene:  ATP1A1
AT1A1_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


Thu Jan 10 12:30:21 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/ATP1A1.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 ATP1A1.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/284701
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/284701/ATP1A1.stick_fig.txt ATP1A1.stick_fig.png

Working with gene:  RERE
RERE_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


Thu Jan 10 12:30:27 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/RERE.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 RERE.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/284701
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/284701/RERE.stick_fig.txt RERE.stick_fig.png

Working with gene:  QRICH2
QRIC2_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


Thu Jan 10 12:30:34 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/QRICH2.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 QRICH2.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/284701
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/284701/QRICH2.stick_fig.txt QRICH2.stick_fig.png

Working with gene:  SLC5A12
SC5AC_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


Thu Jan 10 12:30:41 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/SLC5A12.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 SLC5A12.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/284701
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/284701/SLC5A12.stick_fig.txt SLC5A12.stick_fig.png

Working with gene:  CDC27
CDC27_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


Thu Jan 10 12:30:47 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/CDC27.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 CDC27.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/284701
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/284701/CDC27.stick_fig.txt CDC27.stick_fig.png

Working with gene:  LGI4
LGI4_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


Thu Jan 10 12:30:53 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/LGI4.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 LGI4.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/284701
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/284701/LGI4.stick_fig.txt LGI4.stick_fig.png

Working with gene:  MLL2
MLL2_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


Thu Jan 10 12:31:00 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/MLL2.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 MLL2.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/284701
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/284701/MLL2.stick_fig.txt MLL2.stick_fig.png

Working with gene:  LRBA
LRBA_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


Thu Jan 10 12:31:07 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/LRBA.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 LRBA.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/284701
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/284701/LRBA.stick_fig.txt LRBA.stick_fig.png

Working with gene:  CMYA5
CMYA5_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


Thu Jan 10 12:31:14 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/CMYA5.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 CMYA5.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/284701
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/284701/CMYA5.stick_fig.txt CMYA5.stick_fig.png

Working with gene:  MUC16
MUC16_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


Thu Jan 10 12:31:20 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/MUC16.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 MUC16.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/284701
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/284701/MUC16.stick_fig.txt MUC16.stick_fig.png

Working with gene:  SFRS2IP
SCAFB_HUMAN
Problem with retrieving features for gene: swiss prot ID likely not found in features database.
Working with gene:  SYNE1
SYNE1_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


Thu Jan 10 12:31:26 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/SYNE1.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 SYNE1.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/284701
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/284701/SYNE1.stick_fig.txt SYNE1.stick_fig.png

Working with gene:  MLL3
MLL3_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


Thu Jan 10 12:31:34 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/MLL3.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 MLL3.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/284701
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/284701/MLL3.stick_fig.txt MLL3.stick_fig.png

Working with gene:  FAT1
FAT1_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


Thu Jan 10 12:31:41 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/FAT1.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 FAT1.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/284701
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/284701/FAT1.stick_fig.txt FAT1.stick_fig.png

Working with gene:  EP400
EP400_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


Thu Jan 10 12:31:49 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/EP400.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 EP400.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/284701
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/284701/EP400.stick_fig.txt EP400.stick_fig.png

Working with gene:  BOD1L
BOD1L_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


Thu Jan 10 12:31:59 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/BOD1L.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 BOD1L.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/284701
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/284701/BOD1L.stick_fig.txt BOD1L.stick_fig.png

Working with gene:  MACF1
MACF1_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


Thu Jan 10 12:32:29 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 22765
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/284701/MACF1.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 MACF1.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/284701
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/284701/MACF1.stick_fig.txt MACF1.stick_fig.png

