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


Thu Nov 15 07:50:15 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/BRAF.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file BRAF.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/BRAF.stick_fig.txt BRAF.stick_fig.png

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


Thu Nov 15 07:51:14 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/NRAS.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NRAS.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/NRAS.stick_fig.txt NRAS.stick_fig.png

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


Thu Nov 15 07:52:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/HRAS.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file HRAS.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/HRAS.stick_fig.txt HRAS.stick_fig.png

Working with gene:  EMG1
NEP1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:53:22 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/EMG1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file EMG1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/EMG1.stick_fig.txt EMG1.stick_fig.png

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


Thu Nov 15 07:54:14 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/TG.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TG.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/TG.stick_fig.txt TG.stick_fig.png

Working with gene:  PRB2
Gene PRB2 does not have swiss prot accession ID in MAF file. Skipping gene... 
Working with gene:  EIF1AX
IF1AX_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:54:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/EIF1AX.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file EIF1AX.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/EIF1AX.stick_fig.txt EIF1AX.stick_fig.png

Working with gene:  PTTG1IP
PTTG_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:54:46 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/PTTG1IP.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PTTG1IP.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/PTTG1IP.stick_fig.txt PTTG1IP.stick_fig.png

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


Thu Nov 15 07:55:01 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/MUC7.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MUC7.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/MUC7.stick_fig.txt MUC7.stick_fig.png

Working with gene:  ZNF845
ZN845_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:55:16 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/ZNF845.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ZNF845.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/ZNF845.stick_fig.txt ZNF845.stick_fig.png

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


Thu Nov 15 07:55:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/RPTN.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RPTN.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/RPTN.stick_fig.txt RPTN.stick_fig.png

Working with gene:  PPM1D
PPM1D_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:55:45 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/PPM1D.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PPM1D.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/PPM1D.stick_fig.txt PPM1D.stick_fig.png

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


Thu Nov 15 07:56:01 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/TROAP.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TROAP.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/TROAP.stick_fig.txt TROAP.stick_fig.png

Working with gene:  PRG4
PRG4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:56:16 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/PRG4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PRG4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/PRG4.stick_fig.txt PRG4.stick_fig.png

Working with gene:  FAM47C
FA47C_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:56:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/FAM47C.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FAM47C.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/FAM47C.stick_fig.txt FAM47C.stick_fig.png

Working with gene:  ARID1B
ARI1B_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:56:40 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/ARID1B.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ARID1B.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/ARID1B.stick_fig.txt ARID1B.stick_fig.png

Working with gene:  ZNF799
ZN799_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:56:50 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/ZNF799.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ZNF799.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/ZNF799.stick_fig.txt ZNF799.stick_fig.png

Working with gene:  DNMT3A
DNM3A_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:56:59 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/DNMT3A.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DNMT3A.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/DNMT3A.stick_fig.txt DNMT3A.stick_fig.png

Working with gene:  GPR44
GPR44_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:57:09 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/GPR44.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GPR44.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/GPR44.stick_fig.txt GPR44.stick_fig.png

Working with gene:  R3HDM2
R3HD2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:57:19 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/R3HDM2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file R3HDM2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/R3HDM2.stick_fig.txt R3HDM2.stick_fig.png

Working with gene:  CCDC15
CCD15_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:57:28 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/CCDC15.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CCDC15.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/CCDC15.stick_fig.txt CCDC15.stick_fig.png

Working with gene:  ZNF780A
Z780A_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:57:37 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/ZNF780A.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ZNF780A.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/ZNF780A.stick_fig.txt ZNF780A.stick_fig.png

Working with gene:  MLL3
MLL3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:57:46 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/MLL3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MLL3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/MLL3.stick_fig.txt MLL3.stick_fig.png

Working with gene:  ZFHX3
ZFHX3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:57:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/ZFHX3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ZFHX3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/ZFHX3.stick_fig.txt ZFHX3.stick_fig.png

Working with gene:  DICER1
DICER_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:58:07 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/DICER1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DICER1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/DICER1.stick_fig.txt DICER1.stick_fig.png

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


Thu Nov 15 07:58:21 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/COL5A3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file COL5A3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/COL5A3.stick_fig.txt COL5A3.stick_fig.png

Working with gene:  ZNF208
Gene ZNF208 does not have swiss prot accession ID in MAF file. Skipping gene... 
Working with gene:  CD209
CD209_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Thu Nov 15 07:58:34 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25698
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/CD209.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CD209.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/237867/CD209.stick_fig.txt CD209.stick_fig.png

