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


Tue Oct  9 19:25:28 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/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/181306
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/181306/TP53.stick_fig.txt TP53.stick_fig.png

Working with gene:  ACVR2A
AVR2A_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


Tue Oct  9 19:26:02 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/ACVR2A.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 ACVR2A.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/181306
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/181306/ACVR2A.stick_fig.txt ACVR2A.stick_fig.png

Working with gene:  CBWD1
Gene CBWD1 does not have swiss prot accession ID in MAF file. Skipping gene... 
Working with gene:  KRAS
RASK_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


Tue Oct  9 19:26:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/KRAS.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 KRAS.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/181306
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/181306/KRAS.stick_fig.txt KRAS.stick_fig.png

Working with gene:  TRIM48
TRI48_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


Tue Oct  9 19:27:00 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/TRIM48.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 TRIM48.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/181306
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/181306/TRIM48.stick_fig.txt TRIM48.stick_fig.png

Working with gene:  RPL22
RL22_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


Tue Oct  9 19:27:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/RPL22.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 RPL22.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/181306
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/181306/RPL22.stick_fig.txt RPL22.stick_fig.png

Working with gene:  SFRS12IP1
SR1IP_HUMAN
Problem with retrieving features for gene: swiss prot ID likely not found in features database.
Working with gene:  SMAP1
SMAP1_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


Tue Oct  9 19:27:59 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/SMAP1.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 SMAP1.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/181306
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/181306/SMAP1.stick_fig.txt SMAP1.stick_fig.png

Working with gene:  DNAJC15
DJC15_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


Tue Oct  9 19:28:28 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/DNAJC15.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 DNAJC15.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/181306
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/181306/DNAJC15.stick_fig.txt DNAJC15.stick_fig.png

Working with gene:  ZNF48
ZNF48_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


Tue Oct  9 19:28:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/ZNF48.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 ZNF48.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/181306
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/181306/ZNF48.stick_fig.txt ZNF48.stick_fig.png

Working with gene:  EFNA2
EFNA2_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


Tue Oct  9 19:29:24 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/EFNA2.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 EFNA2.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/181306
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/181306/EFNA2.stick_fig.txt EFNA2.stick_fig.png

Working with gene:  NSF
NSF_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


Tue Oct  9 19:29:53 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/NSF.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 NSF.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/181306
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/181306/NSF.stick_fig.txt NSF.stick_fig.png

Working with gene:  HPGDS
HPGDS_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


Tue Oct  9 19:30:21 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/HPGDS.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 HPGDS.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/181306
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/181306/HPGDS.stick_fig.txt HPGDS.stick_fig.png

Working with gene:  PGM5
PGM5_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


Tue Oct  9 19:30:50 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/PGM5.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 PGM5.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/181306
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/181306/PGM5.stick_fig.txt PGM5.stick_fig.png

Working with gene:  ARID1A
ARI1A_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


Tue Oct  9 19:31:18 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/ARID1A.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 ARID1A.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/181306
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/181306/ARID1A.stick_fig.txt ARID1A.stick_fig.png

Working with gene:  RHOA
RHOA_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


Tue Oct  9 19:31:48 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/RHOA.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 RHOA.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/181306
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/181306/RHOA.stick_fig.txt RHOA.stick_fig.png

Working with gene:  PIK3CA
PK3CA_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


Tue Oct  9 19:32:16 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/PIK3CA.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 PIK3CA.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/181306
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/181306/PIK3CA.stick_fig.txt PIK3CA.stick_fig.png

Working with gene:  INO80E
IN80E_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


Tue Oct  9 19:32:47 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/INO80E.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 INO80E.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/181306
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/181306/INO80E.stick_fig.txt INO80E.stick_fig.png

Working with gene:  FGF22
FGF22_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


Tue Oct  9 19:33:15 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/FGF22.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 FGF22.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/181306
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/181306/FGF22.stick_fig.txt FGF22.stick_fig.png

Working with gene:  OR8H3
OR8H3_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


Tue Oct  9 19:33:43 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/OR8H3.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 OR8H3.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/181306
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/181306/OR8H3.stick_fig.txt OR8H3.stick_fig.png

Working with gene:  ZNF804B
Z804B_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


Tue Oct  9 19:34:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/ZNF804B.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 ZNF804B.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/181306
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/181306/ZNF804B.stick_fig.txt ZNF804B.stick_fig.png

Working with gene:  CDH1
CADH1_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


Tue Oct  9 19:34:43 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/CDH1.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 CDH1.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/181306
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/181306/CDH1.stick_fig.txt CDH1.stick_fig.png

Working with gene:  TUSC3
TUSC3_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


Tue Oct  9 19:35:13 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/TUSC3.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 TUSC3.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/181306
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/181306/TUSC3.stick_fig.txt TUSC3.stick_fig.png

Working with gene:  PRRT2
PRRT2_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


Tue Oct  9 19:35:43 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/PRRT2.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 PRRT2.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/181306
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/181306/PRRT2.stick_fig.txt PRRT2.stick_fig.png

Working with gene:  PTH2
TIP39_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


Tue Oct  9 19:36:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/PTH2.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/181306
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/181306/PTH2.stick_fig.txt PTH2.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/181306/PTH2.stick_fig.txt', 'PTH2.stick_fig.png']' returned non-zero exit status 255

Working with gene:  C17orf63
CQ063_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


Tue Oct  9 19:36:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/C17orf63.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 C17orf63.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/181306
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/181306/C17orf63.stick_fig.txt C17orf63.stick_fig.png

Working with gene:  IAPP
IAPP_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


Tue Oct  9 19:37:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/IAPP.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/181306
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/181306/IAPP.stick_fig.txt IAPP.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/181306/IAPP.stick_fig.txt', 'IAPP.stick_fig.png']' returned non-zero exit status 255

Working with gene:  IRF2
IRF2_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


Tue Oct  9 19:37:27 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/IRF2.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 IRF2.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/181306
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/181306/IRF2.stick_fig.txt IRF2.stick_fig.png

Working with gene:  RNF43
RNF43_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


Tue Oct  9 19:37:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/RNF43.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 RNF43.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/181306
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/181306/RNF43.stick_fig.txt RNF43.stick_fig.png

Working with gene:  HLA-B
Gene HLA-B does not have swiss prot accession ID in MAF file. Skipping gene... 
Working with gene:  HLA-A
1A01_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


Tue Oct  9 19:38:25 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/HLA-A.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 HLA-A.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/181306
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/181306/HLA-A.stick_fig.txt HLA-A.stick_fig.png

Working with gene:  SMAD4
SMAD4_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


Tue Oct  9 19:38:54 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/SMAD4.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 SMAD4.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/181306
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/181306/SMAD4.stick_fig.txt SMAD4.stick_fig.png

Working with gene:  UPF3A
REN3A_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


Tue Oct  9 19:39:23 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/UPF3A.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 UPF3A.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/181306
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/181306/UPF3A.stick_fig.txt UPF3A.stick_fig.png

Working with gene:  CCDC43
CCD43_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


Tue Oct  9 19:39:52 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/CCDC43.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 CCDC43.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/181306
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/181306/CCDC43.stick_fig.txt CCDC43.stick_fig.png

Working with gene:  PHF2
PHF2_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


Tue Oct  9 19:40:20 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/PHF2.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 PHF2.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/181306
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/181306/PHF2.stick_fig.txt PHF2.stick_fig.png

Working with gene:  PCDH15
PCD15_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


Tue Oct  9 19:40:48 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/PCDH15.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 PCDH15.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/181306
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/181306/PCDH15.stick_fig.txt PCDH15.stick_fig.png

Working with gene:  SPRYD5
SPRY5_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


Tue Oct  9 19:41:18 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/SPRYD5.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 SPRYD5.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/181306
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/181306/SPRYD5.stick_fig.txt SPRYD5.stick_fig.png

Working with gene:  SOX1
SOX1_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


Tue Oct  9 19:41:46 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/SOX1.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 SOX1.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/181306
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/181306/SOX1.stick_fig.txt SOX1.stick_fig.png

Working with gene:  POTEG
POTEG_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


Tue Oct  9 19:42:16 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/POTEG.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 POTEG.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/181306
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/181306/POTEG.stick_fig.txt POTEG.stick_fig.png

Working with gene:  TPTE
TPTE_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


Tue Oct  9 19:42:44 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/TPTE.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 TPTE.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/181306
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/181306/TPTE.stick_fig.txt TPTE.stick_fig.png

Working with gene:  FSHR
FSHR_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


Tue Oct  9 19:43:13 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/FSHR.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 FSHR.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/181306
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/181306/FSHR.stick_fig.txt FSHR.stick_fig.png

Working with gene:  UNC93B1
UN93B_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


Tue Oct  9 19:43:42 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/UNC93B1.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 UNC93B1.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/181306
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/181306/UNC93B1.stick_fig.txt UNC93B1.stick_fig.png

Working with gene:  EDNRB
EDNRB_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


Tue Oct  9 19:44:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/EDNRB.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 EDNRB.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/181306
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/181306/EDNRB.stick_fig.txt EDNRB.stick_fig.png

Working with gene:  MARCKS
MARCS_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


Tue Oct  9 19:44:40 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/MARCKS.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 MARCKS.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/181306
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/181306/MARCKS.stick_fig.txt MARCKS.stick_fig.png

Working with gene:  RASA1
RASA1_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


Tue Oct  9 19:45:09 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/RASA1.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 RASA1.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/181306
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/181306/RASA1.stick_fig.txt RASA1.stick_fig.png

Working with gene:  KDM4B
KDM4B_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


Tue Oct  9 19:45:38 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/KDM4B.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 KDM4B.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/181306
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/181306/KDM4B.stick_fig.txt KDM4B.stick_fig.png

Working with gene:  LHCGR
LSHR_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


Tue Oct  9 19:45:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/LHCGR.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 LHCGR.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/181306
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/181306/LHCGR.stick_fig.txt LHCGR.stick_fig.png

Working with gene:  TM7SF4
TM7S4_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


Tue Oct  9 19:46:00 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/TM7SF4.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 TM7SF4.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/181306
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/181306/TM7SF4.stick_fig.txt TM7SF4.stick_fig.png

Working with gene:  TLR4
TLR4_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


Tue Oct  9 19:46:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/TLR4.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 TLR4.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/181306
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/181306/TLR4.stick_fig.txt TLR4.stick_fig.png

Working with gene:  IL2RG
IL2RG_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


Tue Oct  9 19:46:23 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/IL2RG.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 IL2RG.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/181306
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/181306/IL2RG.stick_fig.txt IL2RG.stick_fig.png

Working with gene:  TSHZ2
TSH2_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


Tue Oct  9 19:46:34 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/TSHZ2.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 TSHZ2.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/181306
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/181306/TSHZ2.stick_fig.txt TSHZ2.stick_fig.png

Working with gene:  PDZRN4
PZRN4_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


Tue Oct  9 19:46:46 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/PDZRN4.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 PDZRN4.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/181306
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/181306/PDZRN4.stick_fig.txt PDZRN4.stick_fig.png

Working with gene:  POM121L12
P1L12_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


Tue Oct  9 19:46:58 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/POM121L12.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 POM121L12.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/181306
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/181306/POM121L12.stick_fig.txt POM121L12.stick_fig.png

Working with gene:  WBSCR17
GLTL3_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


Tue Oct  9 19:47:09 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/WBSCR17.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 WBSCR17.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/181306
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/181306/WBSCR17.stick_fig.txt WBSCR17.stick_fig.png

Working with gene:  ZC4H2
ZC4H2_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


Tue Oct  9 19:47:20 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23694
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181306/ZC4H2.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 ZC4H2.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/181306
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/181306/ZC4H2.stick_fig.txt ZC4H2.stick_fig.png

