2019-12-16 11:39:09 PM::INFO  Working with gene: TP53
2019-12-16 11:39:21 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.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
2019-12-16 11:39:28 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.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
2019-12-16 11:39:28 PM::INFO  Working with gene: CDKN2A
2019-12-16 11:39:35 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/CDKN2A.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 CDKN2A.stick_fig.jpg
Done
2019-12-16 11:39:41 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/CDKN2A.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 CDKN2A.stick_fig.pdf
Done
2019-12-16 11:39:41 PM::INFO  Working with gene: PTEN
2019-12-16 11:39:48 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
2019-12-16 11:39:55 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
2019-12-16 11:39:55 PM::INFO  Working with gene: KMT2D
2019-12-16 11:40:03 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.113
Processing input file /cromwell_root/KMT2D.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 KMT2D.stick_fig.jpg
Done
2019-12-16 11:40:10 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.129
Processing input file /cromwell_root/KMT2D.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 KMT2D.stick_fig.pdf
Done
2019-12-16 11:40:10 PM::INFO  Working with gene: NFE2L2
2019-12-16 11:40:18 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/NFE2L2.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:
'Basic motif. {ECO:0000255|PROSITE- ProRule:PRU0097'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU0'} 
{> In mutfig at 516} 
Generating output file NFE2L2.stick_fig.jpg
Done
2019-12-16 11:40:24 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/NFE2L2.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:
'Basic motif. {ECO:0000255|PROSITE- ProRule:PRU0097'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU0'} 
{> In mutfig at 516} 
Generating output file NFE2L2.stick_fig.pdf
Done
2019-12-16 11:40:24 PM::INFO  Working with gene: ARID1A
2019-12-16 11:40:31 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/ARID1A.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:
'Nuclear localization signal. {ECO:0000269|PubMed:2'} 
{> In mutfig at 516} 
Generating output file ARID1A.stick_fig.jpg
Done
2019-12-16 11:40:37 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/ARID1A.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:
'Nuclear localization signal. {ECO:0000269|PubMed:2'} 
{> In mutfig at 516} 
Generating output file ARID1A.stick_fig.pdf
Done
2019-12-16 11:40:37 PM::INFO  Working with gene: NOTCH1
2019-12-16 11:40:43 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/NOTCH1.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 DLL4. {ECO:0000250|UniProtKB:Q070'} 
{> In mutfig at 516} 
Generating output file NOTCH1.stick_fig.jpg
Done
2019-12-16 11:40:50 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/NOTCH1.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 DLL4. {ECO:0000250|UniProtKB:Q070'} 
{> In mutfig at 516} 
Generating output file NOTCH1.stick_fig.pdf
Done
2019-12-16 11:40:50 PM::INFO  Working with gene: NF1
2019-12-16 11:40:57 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.241
Processing input file /cromwell_root/NF1.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 NF1.stick_fig.jpg
Done
2019-12-16 11:41:05 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.257
Processing input file /cromwell_root/NF1.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 NF1.stick_fig.pdf
Done
2019-12-16 11:41:05 PM::INFO  Working with gene: CUL3
2019-12-16 11:41:11 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.273
Processing input file /cromwell_root/CUL3.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 CUL3.stick_fig.jpg
Done
2019-12-16 11:41:18 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.289
Processing input file /cromwell_root/CUL3.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 CUL3.stick_fig.pdf
Done
2019-12-16 11:41:18 PM::INFO  Working with gene: KEAP1
2019-12-16 11:41:24 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.305
Processing input file /cromwell_root/KEAP1.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 KEAP1.stick_fig.jpg
Done
2019-12-16 11:41:31 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.321
Processing input file /cromwell_root/KEAP1.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 KEAP1.stick_fig.pdf
Done
2019-12-16 11:41:31 PM::INFO  Working with gene: KRAS
2019-12-16 11:41:37 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.337
Processing input file /cromwell_root/KRAS.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:
'GTP. {ECO:0000269|PubMed:22431598, ECO:0000269|Pub'} 
{> In mutfig at 516} 
Generating output file KRAS.stick_fig.jpg
Done
2019-12-16 11:41:43 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.353
Processing input file /cromwell_root/KRAS.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:
'GTP. {ECO:0000269|PubMed:22431598, ECO:0000269|Pub'} 
{> In mutfig at 516} 
Generating output file KRAS.stick_fig.pdf
Done
2019-12-16 11:41:43 PM::INFO  Working with gene: KDM6A
2019-12-16 11:41:50 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.369
Processing input file /cromwell_root/KDM6A.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 KDM6A.stick_fig.jpg
Done
2019-12-16 11:41:56 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.385
Processing input file /cromwell_root/KDM6A.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 KDM6A.stick_fig.pdf
Done
2019-12-16 11:41:56 PM::INFO  Working with gene: RANBP2
2019-12-16 11:42:02 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.401
Processing input file /cromwell_root/RANBP2.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 BICD2. {ECO:0000269|PubMed:203867'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with SUMO1. {ECO:0000269|PubMed:156086'} 
{> In mutfig at 516} 
Generating output file RANBP2.stick_fig.jpg
Done
2019-12-16 11:42:11 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.417
Processing input file /cromwell_root/RANBP2.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 BICD2. {ECO:0000269|PubMed:203867'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with SUMO1. {ECO:0000269|PubMed:156086'} 
{> In mutfig at 516} 
Generating output file RANBP2.stick_fig.pdf
Done
2019-12-16 11:42:11 PM::INFO  Runtime: 3.08066538572 minutes
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.5ee5b4f7/err.6
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.5ee5b4f7/out.6
  adding: KEAP1.stick_fig.jpg (deflated 28%)
  adding: KRAS.stick_fig.pdf (deflated 33%)
  adding: KRAS.stick_fig.jpg (deflated 29%)
  adding: CDKN2A.stick_fig.pdf (deflated 30%)
  adding: RANBP2.stick_fig.txt (deflated 60%)
  adding: ARID1A.stick_fig.jpg (deflated 20%)
  adding: KDM6A.stick_fig.txt (deflated 55%)
  adding: KDM6A.stick_fig.jpg (deflated 34%)
  adding: KMT2D.stick_fig.txt (deflated 71%)
  adding: CDKN2A.stick_fig.txt (deflated 68%)
  adding: KDM6A.stick_fig.pdf (deflated 34%)
  adding: NF1.stick_fig.jpg (deflated 22%)
  adding: ARID1A.stick_fig.txt (deflated 68%)
  adding: RANBP2.stick_fig.jpg (deflated 22%)
  adding: script (deflated 75%)
  adding: NOTCH1.stick_fig.txt (deflated 71%)
  adding: CDKN2A.stick_fig.jpg (deflated 25%)
  adding: NF1.stick_fig.txt (deflated 65%)
  adding: generatedStickFigurePaths.txt (deflated 73%)
  adding: KRAS.stick_fig.txt (deflated 75%)
  adding: PTEN.stick_fig.pdf (deflated 31%)
  adding: KEAP1.stick_fig.pdf (deflated 28%)
  adding: gcs_transfer.sh (deflated 75%)
  adding: CUL3.stick_fig.pdf (deflated 32%)
  adding: TP53.stick_fig.pdf (deflated 14%)
  adding: NOTCH1.stick_fig.jpg (deflated 17%)
  adding: gcs_delocalization.sh (deflated 84%)
  adding: CUL3.stick_fig.jpg (deflated 32%)
  adding: KMT2D.stick_fig.pdf (deflated 23%)
  adding: stderr (stored 0%)
  adding: NFE2L2.stick_fig.pdf (deflated 30%)
  adding: stdout