2019-09-24 09:02:47 PM::INFO  Working with gene: TP53
2019-09-24 09:03:00 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.16
Processing input file /cromwell_root/TP53.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
{Warning: incomplete command in TeX text string:
'Interaction with CCAR2. {ECO:0000269|PubMed:257328'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with HRMT1L2. {ECO:0000269|PubMed:1518'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Required for interaction with ZNF385A. {ECO:000026'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Required for interaction with FBXO42. {ECO:0000269'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with E4F1. {ECO:0000269|PubMed:1064499'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with CARM1. {ECO:0000269|PubMed:151867'} 
{> In mutfig at 516} 
Generating output file TP53.stick_fig.jpg
Done
2019-09-24 09:03:07 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.33
Processing input file /cromwell_root/TP53.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
{Warning: incomplete command in TeX text string:
'Interaction with CCAR2. {ECO:0000269|PubMed:257328'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with HRMT1L2. {ECO:0000269|PubMed:1518'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Required for interaction with ZNF385A. {ECO:000026'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Required for interaction with FBXO42. {ECO:0000269'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with E4F1. {ECO:0000269|PubMed:1064499'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with CARM1. {ECO:0000269|PubMed:151867'} 
{> In mutfig at 516} 
Generating output file TP53.stick_fig.pdf
Done
2019-09-24 09:03:07 PM::INFO  Working with gene: PIK3CA
2019-09-24 09:03:14 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.49
Processing input file /cromwell_root/PIK3CA.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file PIK3CA.stick_fig.jpg
Done
2019-09-24 09:03:21 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.65
Processing input file /cromwell_root/PIK3CA.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file PIK3CA.stick_fig.pdf
Done
2019-09-24 09:03:21 PM::INFO  Working with gene: PTEN
2019-09-24 09:03:28 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.81
Processing input file /cromwell_root/PTEN.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
{Warning: incomplete command in TeX text string:
'Required for interaction with NOP53. {ECO:0000269|'} 
{> In mutfig at 516} 
Generating output file PTEN.stick_fig.jpg
Done
2019-09-24 09:03:34 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.97
Processing input file /cromwell_root/PTEN.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
{Warning: incomplete command in TeX text string:
'Required for interaction with NOP53. {ECO:0000269|'} 
{> In mutfig at 516} 
Generating output file PTEN.stick_fig.pdf
Done
2019-09-24 09:03:34 PM::INFO  Working with gene: CDH1
2019-09-24 09:03:42 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.113
Processing input file /cromwell_root/CDH1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file CDH1.stick_fig.jpg
Done
2019-09-24 09:03:49 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.129
Processing input file /cromwell_root/CDH1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file CDH1.stick_fig.pdf
Done
2019-09-24 09:03:49 PM::INFO  Working with gene: MAP3K1
2019-09-24 09:03:57 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.145
Processing input file /cromwell_root/MAP3K1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file MAP3K1.stick_fig.jpg
Done
2019-09-24 09:04:03 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.161
Processing input file /cromwell_root/MAP3K1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file MAP3K1.stick_fig.pdf
Done
2019-09-24 09:04:03 PM::INFO  Working with gene: AKT1
2019-09-24 09:04:10 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.177
Processing input file /cromwell_root/AKT1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file AKT1.stick_fig.jpg
Done
2019-09-24 09:04:16 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.193
Processing input file /cromwell_root/AKT1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file AKT1.stick_fig.pdf
Done
2019-09-24 09:04:16 PM::INFO  Working with gene: GATA3
2019-09-24 09:04:23 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.209
Processing input file /cromwell_root/GATA3.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file GATA3.stick_fig.jpg
Done
2019-09-24 09:04:29 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.225
Processing input file /cromwell_root/GATA3.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file GATA3.stick_fig.pdf
Done
2019-09-24 09:04:29 PM::INFO  Runtime: 1.78141371806 minutes
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.8b336fed/out.6
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.8b336fed/err.6
  adding: AKT1.stick_fig.txt (deflated 65%)
  adding: generatedStickFigurePaths.txt (deflated 68%)
  adding: TP53.stick_fig.jpg (deflated 9%)
  adding: MAP3K1.stick_fig.pdf (deflated 27%)
  adding: AKT1.stick_fig.jpg (deflated 37%)
  adding: PIK3CA.stick_fig.txt (deflated 86%)
  adding: MAP3K1.stick_fig.txt (deflated 67%)
  adding: TP53.stick_fig.pdf (deflated 16%)
  adding: gcs_delocalization.sh (deflated 85%)
  adding: PTEN.stick_fig.txt (deflated 60%)
  adding: gcs_localization.sh (deflated 76%)
  adding: MAP3K1.stick_fig.jpg (deflated 19%)
  adding: gcs_transfer.sh (deflated 74%)
  adding: GATA3.stick_fig.pdf (deflated 34%)
  adding: CDH1.stick_fig.jpg (deflated 21%)
  adding: stderr (stored 0%)
  adding: CDH1.stick_fig.pdf (deflated 30%)
  adding: PIK3CA.stick_fig.jpg (deflated 43%)
  adding: GATA3.stick_fig.jpg (deflated 31%)
  adding: fc-secure-823808d0-5404-49c9-990f-b3d9e353e468/ (stored 0%)
  adding: fc-secure-823808d0-5404-49c9-990f-b3d9e353e468/7a5024b9-1b0a-4d68-b14f-ad883e9c52ed/ (stored 0%)
  adding: fc-secure-823808d0-5404-49c9-990f-b3d9e353e468/7a5024b9-1b0a-4d68-b14f-ad883e9c52ed/mutation_mutsig2cv_hg19/ (stored 0%)
  adding: fc-secure-823808d0-5404-49c9-990f-b3d9e353e468/7a5024b9-1b0a-4d68-b14f-ad883e9c52ed/mutation_mutsig2cv_hg19/c97c1d7c-6a7e-448f-b968-82487f7b2d8a/ (stored 0%)
  adding: fc-secure-823808d0-5404-49c9-990f-b3d9e353e468/7a5024b9-1b0a-4d68-b14f-ad883e9c52ed/mutation_mutsig2cv_hg19/c97c1d7c-6a7e-448f-b968-82487f7b2d8a/call-tool_mutsig2cv_hg19/ (stored 0%)
  adding: fc-secure-823808d0-5404-49c9-990f-b3d9e353e468/7a5024b9-1b0a-4d68-b14f-ad883e9c52ed/mutation_mutsig2cv_hg19/c97c1d7c-6a7e-448f-b968-82487f7b2d8a/call-tool_mutsig2cv_hg19/sig_genes.txt (deflated 74%)
  adding: fc-secure-823808d0-5404-49c9-990f-b3d9e353e468/7a5024b9-1b0a-4d68-b14f-ad883e9c52ed/mutation_mutsig2cv_hg19/c97c1d7c-6a7e-448f-b968-82487f7b2d8a/call-tool_mutsig2cv_hg19/BRCA-noHyper.final_analysis_set.maf (deflated 78%)
  adding: AKT1.stick_fig.pdf (deflated 35%)
  adding: PTEN.stick_fig.pdf (deflated 33%)
  adding: PIK3CA.stick_fig.pdf (deflated 24%)
  adding: TP53.stick_fig.txt (deflated 78%)
  adding: CDH1.stick_fig.txt (deflated 65%)
  adding: stdout