2020-09-25 07:06:53 PM::INFO  Working with gene: TP53
2020-09-25 07:07:10 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.15
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
2020-09-25 07:07:19 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.32
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
2020-09-25 07:07:19 PM::INFO  Working with gene: KMT2D
2020-09-25 07:07:27 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.48
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
2020-09-25 07:07:34 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.64
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
2020-09-25 07:07:34 PM::INFO  Working with gene: CDKN2A
2020-09-25 07:07:42 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.80
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
2020-09-25 07:07:50 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.96
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
2020-09-25 07:07:50 PM::INFO  Working with gene: USP13
2020-09-25 07:07:57 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.112
Processing input file /cromwell_root/USP13.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 USP13.stick_fig.jpg
Done
2020-09-25 07:08:04 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.128
Processing input file /cromwell_root/USP13.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 USP13.stick_fig.pdf
Done
2020-09-25 07:08:04 PM::INFO  Working with gene: KEAP1
2020-09-25 07:08:11 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.144
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
2020-09-25 07:08:18 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.160
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
2020-09-25 07:08:18 PM::INFO  Working with gene: NFE2L2
2020-09-25 07:08:26 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.176
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
2020-09-25 07:08:33 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.192
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
2020-09-25 07:08:33 PM::INFO  Runtime: 1.77065200011 minutes
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.99cf94d3/err.1
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.99cf94d3/out.1
  adding: USP13.stick_fig.jpg (deflated 35%)
  adding: KMT2D.stick_fig.jpg (deflated 15%)
  adding: TP53.stick_fig.jpg (deflated 11%)
  adding: KEAP1.stick_fig.txt (deflated 73%)
  adding: CDKN2A.stick_fig.txt (deflated 61%)
  adding: generatedStickFigurePaths.txt (deflated 66%)
  adding: TP53.stick_fig.pdf (deflated 14%)
  adding: NFE2L2.stick_fig.txt (deflated 71%)
  adding: stderr (stored 0%)
  adding: script (deflated 75%)
  adding: gcs_transfer.sh (deflated 74%)
  adding: NFE2L2.stick_fig.jpg (deflated 23%)
  adding: CDKN2A.stick_fig.jpg (deflated 34%)
  adding: KMT2D.stick_fig.txt (deflated 73%)
  adding: CDKN2A.stick_fig.pdf (deflated 34%)
  adding: KEAP1.stick_fig.pdf (deflated 29%)
  adding: gcs_delocalization.sh (deflated 84%)
  adding: USP13.stick_fig.txt (deflated 70%)
  adding: stdout