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


Fri Jan 11 01:50:21 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/EGFR.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file EGFR.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/EGFR.stick_fig.txt EGFR.stick_fig.png

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


Fri Jan 11 01:50:40 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/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/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TP53.stick_fig.txt TP53.stick_fig.png

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


Fri Jan 11 01:50:54 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PTEN.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PTEN.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PTEN.stick_fig.txt PTEN.stick_fig.png

Working with gene:  PIK3R1
P85A_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:51:07 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PIK3R1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PIK3R1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PIK3R1.stick_fig.txt PIK3R1.stick_fig.png

Working with gene:  RB1
RB_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:51:21 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/RB1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RB1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/RB1.stick_fig.txt RB1.stick_fig.png

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


Fri Jan 11 01:51:33 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/NF1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NF1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/NF1.stick_fig.txt NF1.stick_fig.png

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


Fri Jan 11 01:51:46 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/IDH1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file IDH1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/IDH1.stick_fig.txt IDH1.stick_fig.png

Working with gene:  SPTA1
SPTA1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:51:58 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SPTA1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SPTA1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SPTA1.stick_fig.txt SPTA1.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


Fri Jan 11 01:52:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/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/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PIK3CA.stick_fig.txt PIK3CA.stick_fig.png

Working with gene:  GABRA6
GBRA6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:52:25 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GABRA6.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GABRA6.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GABRA6.stick_fig.txt GABRA6.stick_fig.png

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


Fri Jan 11 01:52:37 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/FLG.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FLG.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/FLG.stick_fig.txt FLG.stick_fig.png

Working with gene:  RPL5
RL5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:52:50 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/RPL5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RPL5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/RPL5.stick_fig.txt RPL5.stick_fig.png

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


Fri Jan 11 01:53:02 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KEL.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file KEL.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KEL.stick_fig.txt KEL.stick_fig.png

Working with gene:  RIMS2
RIMS2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:53:15 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/RIMS2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RIMS2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/RIMS2.stick_fig.txt RIMS2.stick_fig.png

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


Fri Jan 11 01:53:28 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PCLO.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PCLO.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PCLO.stick_fig.txt PCLO.stick_fig.png

Working with gene:  RBM47
RBM47_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:53:41 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/RBM47.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RBM47.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/RBM47.stick_fig.txt RBM47.stick_fig.png

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


Fri Jan 11 01:53:53 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TCHH.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TCHH.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TCHH.stick_fig.txt TCHH.stick_fig.png

Working with gene:  SEMA3C
SEM3C_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:54:05 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SEMA3C.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SEMA3C.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SEMA3C.stick_fig.txt SEMA3C.stick_fig.png

Working with gene:  OR8K3
OR8K3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:54:18 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR8K3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR8K3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR8K3.stick_fig.txt OR8K3.stick_fig.png

Working with gene:  PRB2
Gene PRB2 does not have swiss prot accession ID in MAF file. Skipping gene... 
Working with gene:  RYR2
RYR2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:54:31 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/RYR2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file RYR2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/RYR2.stick_fig.txt RYR2.stick_fig.png

Working with gene:  TPTE2
TPTE2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:54:44 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TPTE2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TPTE2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TPTE2.stick_fig.txt TPTE2.stick_fig.png

Working with gene:  LZTR1
LZTR1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:54:56 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/LZTR1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LZTR1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/LZTR1.stick_fig.txt LZTR1.stick_fig.png

Working with gene:  DCAF12L2
DC122_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:55:08 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/DCAF12L2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DCAF12L2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/DCAF12L2.stick_fig.txt DCAF12L2.stick_fig.png

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


Fri Jan 11 01:55:21 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PSPH.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PSPH.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PSPH.stick_fig.txt PSPH.stick_fig.png

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


Fri Jan 11 01:55:32 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PDGFRA.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PDGFRA.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PDGFRA.stick_fig.txt PDGFRA.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


Fri Jan 11 01:55:42 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/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/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SPRYD5.stick_fig.txt SPRYD5.stick_fig.png

Working with gene:  LRFN5
LRFN5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:55:51 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/LRFN5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LRFN5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/LRFN5.stick_fig.txt LRFN5.stick_fig.png

Working with gene:  MUC16
MUC16_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:56:01 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/MUC16.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MUC16.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/MUC16.stick_fig.txt MUC16.stick_fig.png

Working with gene:  CALN1
CABP8_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:56:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CALN1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CALN1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CALN1.stick_fig.txt CALN1.stick_fig.png

Working with gene:  HCN1
HCN1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:56:22 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/HCN1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file HCN1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/HCN1.stick_fig.txt HCN1.stick_fig.png

Working with gene:  KIF2B
KIF2B_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:56:31 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KIF2B.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file KIF2B.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KIF2B.stick_fig.txt KIF2B.stick_fig.png

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


Fri Jan 11 01:56:41 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/MUC17.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MUC17.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/MUC17.stick_fig.txt MUC17.stick_fig.png

Working with gene:  AZGP1
ZA2G_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:56:51 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/AZGP1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file AZGP1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/AZGP1.stick_fig.txt AZGP1.stick_fig.png

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


Fri Jan 11 01:57:00 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/AFM.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file AFM.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/AFM.stick_fig.txt AFM.stick_fig.png

Working with gene:  OR5D13
OR5DD_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:57:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5D13.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR5D13.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5D13.stick_fig.txt OR5D13.stick_fig.png

Working with gene:  SULT1B1
ST1B1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:57:22 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SULT1B1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SULT1B1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SULT1B1.stick_fig.txt SULT1B1.stick_fig.png

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


Fri Jan 11 01:57:31 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SEMG1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SEMG1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SEMG1.stick_fig.txt SEMG1.stick_fig.png

Working with gene:  DRD5
DRD5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:57:41 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/DRD5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DRD5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/DRD5.stick_fig.txt DRD5.stick_fig.png

Working with gene:  OR5D18
OR5DI_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:57:51 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5D18.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR5D18.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5D18.stick_fig.txt OR5D18.stick_fig.png

Working with gene:  TRPV6
TRPV6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:58:01 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TRPV6.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TRPV6.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TRPV6.stick_fig.txt TRPV6.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


Fri Jan 11 01:58:11 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/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/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/POM121L12.stick_fig.txt POM121L12.stick_fig.png

Working with gene:  COL1A2
CO1A2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:58:22 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/COL1A2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file COL1A2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/COL1A2.stick_fig.txt COL1A2.stick_fig.png

Working with gene:  LRRC55
LRC55_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:58:36 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/LRRC55.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LRRC55.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/LRRC55.stick_fig.txt LRRC55.stick_fig.png

Working with gene:  OR4D5
OR4D5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:58:46 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR4D5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR4D5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR4D5.stick_fig.txt OR4D5.stick_fig.png

Working with gene:  CNTNAP2
CNTP2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:58:56 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CNTNAP2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CNTNAP2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CNTNAP2.stick_fig.txt CNTNAP2.stick_fig.png

Working with gene:  WNT2
WNT2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:59:07 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/WNT2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file WNT2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/WNT2.stick_fig.txt WNT2.stick_fig.png

Working with gene:  GABRA1
GBRA1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:59:17 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GABRA1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GABRA1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GABRA1.stick_fig.txt GABRA1.stick_fig.png

Working with gene:  OR5W2
OR5W2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:59:28 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5W2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR5W2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5W2.stick_fig.txt OR5W2.stick_fig.png

Working with gene:  SLC1A6
EAA4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:59:37 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SLC1A6.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SLC1A6.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SLC1A6.stick_fig.txt SLC1A6.stick_fig.png

Working with gene:  DOCK5
DOCK5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:59:47 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/DOCK5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DOCK5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/DOCK5.stick_fig.txt DOCK5.stick_fig.png

Working with gene:  HMCN1
HMCN1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 01:59:57 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/HMCN1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file HMCN1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/HMCN1.stick_fig.txt HMCN1.stick_fig.png

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


Fri Jan 11 02:00:08 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/UGT2A3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file UGT2A3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/UGT2A3.stick_fig.txt UGT2A3.stick_fig.png

Working with gene:  STAG2
STAG2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:00:23 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/STAG2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file STAG2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/STAG2.stick_fig.txt STAG2.stick_fig.png

Working with gene:  CDKN2C
CDN2C_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:00:33 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CDKN2C.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CDKN2C.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CDKN2C.stick_fig.txt CDKN2C.stick_fig.png

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


Fri Jan 11 02:00:43 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/REN.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file REN.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/REN.stick_fig.txt REN.stick_fig.png

Working with gene:  CDC27
CDC27_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:00:52 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CDC27.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CDC27.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CDC27.stick_fig.txt CDC27.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


Fri Jan 11 02:01:02 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/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/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/WBSCR17.stick_fig.txt WBSCR17.stick_fig.png

Working with gene:  GRM3
GRM3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:01:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GRM3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GRM3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GRM3.stick_fig.txt GRM3.stick_fig.png

Working with gene:  KLF17
KLF17_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:01:22 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KLF17.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file KLF17.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KLF17.stick_fig.txt KLF17.stick_fig.png

Working with gene:  FOXG1
FOXG1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:01:32 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/FOXG1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FOXG1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/FOXG1.stick_fig.txt FOXG1.stick_fig.png

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


Fri Jan 11 02:01:41 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/UGT2B28.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file UGT2B28.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/UGT2B28.stick_fig.txt UGT2B28.stick_fig.png

Working with gene:  SLCO6A1
SO6A1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:01:50 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SLCO6A1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SLCO6A1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SLCO6A1.stick_fig.txt SLCO6A1.stick_fig.png

Working with gene:  HIST1H2BE
H2B1C_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:02:01 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/HIST1H2BE.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file HIST1H2BE.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/HIST1H2BE.stick_fig.txt HIST1H2BE.stick_fig.png

Working with gene:  AP3S1
AP3S1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:02:10 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/AP3S1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file AP3S1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/AP3S1.stick_fig.txt AP3S1.stick_fig.png

Working with gene:  PROKR2
PKR2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:02:20 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PROKR2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PROKR2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PROKR2.stick_fig.txt PROKR2.stick_fig.png

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


Fri Jan 11 02:02:29 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/DSG3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DSG3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/DSG3.stick_fig.txt DSG3.stick_fig.png

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


Fri Jan 11 02:02:39 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/QKI.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file QKI.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/QKI.stick_fig.txt QKI.stick_fig.png

Working with gene:  TAS2R41
T2R41_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:02:50 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TAS2R41.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TAS2R41.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TAS2R41.stick_fig.txt TAS2R41.stick_fig.png

Working with gene:  PCDHA3
PCDA3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:02:59 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PCDHA3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PCDHA3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PCDHA3.stick_fig.txt PCDHA3.stick_fig.png

Working with gene:  PAN3
PAN3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:03:09 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PAN3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PAN3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PAN3.stick_fig.txt PAN3.stick_fig.png

Working with gene:  HEATR7B2
HTRB2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:03:17 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/HEATR7B2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file HEATR7B2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/HEATR7B2.stick_fig.txt HEATR7B2.stick_fig.png

Working with gene:  COL6A3
CO6A3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:03:27 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/COL6A3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file COL6A3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/COL6A3.stick_fig.txt COL6A3.stick_fig.png

Working with gene:  CYP3A5
CP3A5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:03:38 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CYP3A5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CYP3A5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CYP3A5.stick_fig.txt CYP3A5.stick_fig.png

Working with gene:  ANO9
ANO9_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:03:48 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ANO9.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ANO9.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ANO9.stick_fig.txt ANO9.stick_fig.png

Working with gene:  PLCXD3
PLCX3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:03:59 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PLCXD3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PLCXD3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PLCXD3.stick_fig.txt PLCXD3.stick_fig.png

Working with gene:  OR5D16
OR5DG_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:04:08 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5D16.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR5D16.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5D16.stick_fig.txt OR5D16.stick_fig.png

Working with gene:  NOX4
NOX4_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:04:17 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/NOX4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file NOX4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/NOX4.stick_fig.txt NOX4.stick_fig.png

Working with gene:  KLK6
KLK6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:04:27 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KLK6.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file KLK6.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KLK6.stick_fig.txt KLK6.stick_fig.png

Working with gene:  TMPRSS6
TMPS6_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:04:36 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TMPRSS6.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TMPRSS6.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TMPRSS6.stick_fig.txt TMPRSS6.stick_fig.png

Working with gene:  PODNL1
PONL1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:04:46 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PODNL1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PODNL1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PODNL1.stick_fig.txt PODNL1.stick_fig.png

Working with gene:  OR5AR1
O5AR1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:04:55 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5AR1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR5AR1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5AR1.stick_fig.txt OR5AR1.stick_fig.png

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


Fri Jan 11 02:05:05 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CALCR.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CALCR.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CALCR.stick_fig.txt CALCR.stick_fig.png

Working with gene:  PCDHA1
PCDA1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:05:14 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PCDHA1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PCDHA1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PCDHA1.stick_fig.txt PCDHA1.stick_fig.png

Working with gene:  ADCY5
ADCY5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:05:24 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ADCY5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ADCY5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ADCY5.stick_fig.txt ADCY5.stick_fig.png

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


Fri Jan 11 02:05:33 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TGFA.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TGFA.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TGFA.stick_fig.txt TGFA.stick_fig.png

Working with gene:  GABRB2
GBRB2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:05:43 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GABRB2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GABRB2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GABRB2.stick_fig.txt GABRB2.stick_fig.png

Working with gene:  ADAMTS16
ATS16_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:05:53 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ADAMTS16.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ADAMTS16.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ADAMTS16.stick_fig.txt ADAMTS16.stick_fig.png

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


Fri Jan 11 02:06:02 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/POTEH.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file POTEH.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/POTEH.stick_fig.txt POTEH.stick_fig.png

Working with gene:  OR52M1
O52M1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:06:12 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR52M1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR52M1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR52M1.stick_fig.txt OR52M1.stick_fig.png

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


Fri Jan 11 02:06:22 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/BCOR.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file BCOR.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/BCOR.stick_fig.txt BCOR.stick_fig.png

Working with gene:  TMEM229B
T229B_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:06:33 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TMEM229B.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TMEM229B.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TMEM229B.stick_fig.txt TMEM229B.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


Fri Jan 11 02:06:42 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/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/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TSHZ2.stick_fig.txt TSHZ2.stick_fig.png

Working with gene:  PSG1
PSG1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:06:51 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PSG1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PSG1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PSG1.stick_fig.txt PSG1.stick_fig.png

Working with gene:  FGD5
FGD5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:07:01 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/FGD5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FGD5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/FGD5.stick_fig.txt FGD5.stick_fig.png

Working with gene:  CDH18
CAD18_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:07:11 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CDH18.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file CDH18.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/CDH18.stick_fig.txt CDH18.stick_fig.png

Working with gene:  KDELC2
KDEL2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:07:20 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KDELC2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file KDELC2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KDELC2.stick_fig.txt KDELC2.stick_fig.png

Working with gene:  TREML2
TRML2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:07:30 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TREML2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TREML2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TREML2.stick_fig.txt TREML2.stick_fig.png

Working with gene:  FOXR2
FOXR2_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:07:40 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/FOXR2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file FOXR2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/FOXR2.stick_fig.txt FOXR2.stick_fig.png

Working with gene:  ADAM29
ADA29_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:07:50 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ADAM29.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ADAM29.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ADAM29.stick_fig.txt ADAM29.stick_fig.png

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


Fri Jan 11 02:07:59 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SERPINB4.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file SERPINB4.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/SERPINB4.stick_fig.txt SERPINB4.stick_fig.png

Working with gene:  OR13C5
O13C5_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:08:09 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR13C5.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR13C5.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR13C5.stick_fig.txt OR13C5.stick_fig.png

Working with gene:  OR5A1
OR5A1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:08:18 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5A1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR5A1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5A1.stick_fig.txt OR5A1.stick_fig.png

Working with gene:  DPP10
DPP10_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:08:27 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/DPP10.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file DPP10.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/DPP10.stick_fig.txt DPP10.stick_fig.png

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


Fri Jan 11 02:08:37 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KPRP.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file KPRP.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/KPRP.stick_fig.txt KPRP.stick_fig.png

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


Fri Jan 11 02:08:47 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/LUM.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file LUM.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/LUM.stick_fig.txt LUM.stick_fig.png

Working with gene:  GNAT3
GNAT3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:08:56 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GNAT3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GNAT3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GNAT3.stick_fig.txt GNAT3.stick_fig.png

Working with gene:  PCDH19
PCD19_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:09:07 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PCDH19.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file PCDH19.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/PCDH19.stick_fig.txt PCDH19.stick_fig.png

Working with gene:  OR5M3
OR5M3_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:09:17 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5M3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file OR5M3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/OR5M3.stick_fig.txt OR5M3.stick_fig.png

Working with gene:  ALPPL2
PPBN_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:09:27 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ALPPL2.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ALPPL2.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ALPPL2.stick_fig.txt ALPPL2.stick_fig.png

Working with gene:  MSL3
MS3L1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:09:37 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/MSL3.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file MSL3.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/MSL3.stick_fig.txt MSL3.stick_fig.png

Working with gene:  GLT1D1
GL1D1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:09:47 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GLT1D1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file GLT1D1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/GLT1D1.stick_fig.txt GLT1D1.stick_fig.png

Working with gene:  ABCB1
MDR1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:09:58 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ABCB1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ABCB1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ABCB1.stick_fig.txt ABCB1.stick_fig.png

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


Fri Jan 11 02:10:08 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TRAT1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file TRAT1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/TRAT1.stick_fig.txt TRAT1.stick_fig.png

Working with gene:  ELTD1
ELTD1_HUMAN
mutfig output: 
Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Fri Jan 11 02:10:18 2013
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 21728
 vncext:      created VNC server for screen 0
Processing input file /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ELTD1.stick_fig.txt
Please ignore the following warning message:
{Warning: Large-scale method does not currently solve this problem formulation,
using medium-scale method instead.} 
> In quadprog at 263
  In find_text_pos at 42
  In mutfig at 322
Generating output file ELTD1.stick_fig.png
Done
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033
mFile: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GenerateStickFigures.6.3863/mutfig /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287033/ELTD1.stick_fig.txt ELTD1.stick_fig.png

