2020-09-24 04:18:50 AM::INFO  Working with gene: TP53
2020-09-24 04:19:04 AM::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
2020-09-24 04:19:11 AM::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
2020-09-24 04:19:11 AM::INFO  Working with gene: KMT2D
2020-09-24 04:19:18 AM::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
2020-09-24 04:19:24 AM::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
2020-09-24 04:19:24 AM::INFO  Working with gene: CDKN2A
2020-09-24 04:19:30 AM::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
2020-09-24 04:19:39 AM::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
2020-09-24 04:19:39 AM::INFO  Working with gene: PTEN
2020-09-24 04:19:45 AM::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/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
2020-09-24 04:19:52 AM::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/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
2020-09-24 04:19:52 AM::INFO  Working with gene: KEAP1
2020-09-24 04:19:58 AM::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
2020-09-24 04:20:04 AM::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
2020-09-24 04:20:04 AM::INFO  Working with gene: NFE2L2
2020-09-24 04:20:11 AM::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
2020-09-24 04:20:17 AM::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
2020-09-24 04:20:17 AM::INFO  Working with gene: CUL3
2020-09-24 04:20:24 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.208
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
2020-09-24 04:20:30 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.224
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
2020-09-24 04:20:30 AM::INFO  Working with gene: FAT1
2020-09-24 04:20:37 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.240
Processing input file /cromwell_root/FAT1.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 FAT1.stick_fig.jpg
Done
2020-09-24 04:20:45 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.256
Processing input file /cromwell_root/FAT1.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 FAT1.stick_fig.pdf
Done
2020-09-24 04:20:45 AM::INFO  Runtime: 2.00435663462 minutes
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.68de0cd3/out.1
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.68de0cd3/err.1
  adding: script (deflated 75%)
  adding: PTEN.stick_fig.jpg (deflated 26%)
  adding: stderr (stored 0%)
  adding: PTEN.stick_fig.txt (deflated 59%)
  adding: KMT2D.stick_fig.jpg (deflated 15%)
  adding: KEAP1.stick_fig.txt (deflated 73%)
  adding: KEAP1.stick_fig.jpg (deflated 28%)
  adding: NFE2L2.stick_fig.jpg (deflated 23%)
  adding: CDKN2A.stick_fig.txt (deflated 61%)
  adding: CUL3.stick_fig.jpg (deflated 36%)
  adding: stdout