2020-06-19 12:29:28 AM::INFO  Working with gene: TP53
2020-06-19 12:29:44 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.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
2020-06-19 12:29:55 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.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
2020-06-19 12:29:55 AM::INFO  Working with gene: PTEN
2020-06-19 12:30:02 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.49
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
2020-06-19 12:30:12 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.65
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
2020-06-19 12:30:12 AM::INFO  Working with gene: ARID1A
2020-06-19 12:30:19 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.81
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
2020-06-19 12:30:28 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.97
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
2020-06-19 12:30:28 AM::INFO  Working with gene: CTCF
2020-06-19 12:30:35 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.113
Processing input file /cromwell_root/CTCF.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 CTCF.stick_fig.jpg
Done
2020-06-19 12:30:42 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.129
Processing input file /cromwell_root/CTCF.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 CTCF.stick_fig.pdf
Done
2020-06-19 12:30:42 AM::INFO  Working with gene: KRAS
2020-06-19 12:30:49 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.145
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
2020-06-19 12:30:56 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.161
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
2020-06-19 12:30:56 AM::INFO  Working with gene: EGFR
2020-06-19 12:31:03 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.177
Processing input file /cromwell_root/EGFR.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 EGFR.stick_fig.jpg
Done
2020-06-19 12:31:13 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.193
Processing input file /cromwell_root/EGFR.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 EGFR.stick_fig.pdf
Done
2020-06-19 12:31:13 AM::INFO  Working with gene: KMT2D
2020-06-19 12:31:21 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.209
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
2020-06-19 12:31:28 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.225
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
2020-06-19 12:31:28 AM::INFO  Working with gene: NF1
2020-06-19 12:31:35 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.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
2020-06-19 12:31:42 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.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
2020-06-19 12:31:42 AM::INFO  Working with gene: RPL22
2020-06-19 12:31:49 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.273
Processing input file /cromwell_root/RPL22.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 RPL22.stick_fig.jpg
Done
2020-06-19 12:31:56 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.289
Processing input file /cromwell_root/RPL22.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 RPL22.stick_fig.pdf
Done
2020-06-19 12:31:56 AM::INFO  Working with gene: STK11
2020-06-19 12:32:04 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.305
Processing input file /cromwell_root/STK11.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:
'Sufficient for interaction with SIRT1. {ECO:000026'} 
{> In mutfig at 516} 
Generating output file STK11.stick_fig.jpg
Done
2020-06-19 12:32:12 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.321
Processing input file /cromwell_root/STK11.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:
'Sufficient for interaction with SIRT1. {ECO:000026'} 
{> In mutfig at 516} 
Generating output file STK11.stick_fig.pdf
Done
2020-06-19 12:32:12 AM::INFO  Working with gene: RB1
2020-06-19 12:32:20 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.337
Processing input file /cromwell_root/RB1.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 LIMD1. {ECO:0000269|PubMed:155425'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Domain C; mediates interaction with E4F1. {ECO:000'} 
{> In mutfig at 516} 
Generating output file RB1.stick_fig.jpg
Done
2020-06-19 12:32:27 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.353
Processing input file /cromwell_root/RB1.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 LIMD1. {ECO:0000269|PubMed:155425'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Domain C; mediates interaction with E4F1. {ECO:000'} 
{> In mutfig at 516} 
Generating output file RB1.stick_fig.pdf
Done
2020-06-19 12:32:27 AM::INFO  Working with gene: CDKN2A
2020-06-19 12:32:35 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.369
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} 
{Warning: incomplete command in TeX text string:
'Interaction with CDK5RAP3 and MDM2. {ECO:0000269|P'} 
{> In mutfig at 516} 
Generating output file CDKN2A.stick_fig.jpg
Done
2020-06-19 12:32:42 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.385
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} 
{Warning: incomplete command in TeX text string:
'Interaction with CDK5RAP3 and MDM2. {ECO:0000269|P'} 
{> In mutfig at 516} 
Generating output file CDKN2A.stick_fig.pdf
Done
2020-06-19 12:32:42 AM::INFO  Working with gene: PIK3CA
2020-06-19 12:32:49 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.401
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
2020-06-19 12:32:56 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.417
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
2020-06-19 12:32:56 AM::INFO  Working with gene: KEAP1
2020-06-19 12:33:03 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.433
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
2020-06-19 12:33:11 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.449
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
2020-06-19 12:33:11 AM::INFO  Working with gene: CTNNB1
2020-06-19 12:33:21 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.465
Processing input file /cromwell_root/CTNNB1.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 BCL9. {ECO:0000269|PubMed:1705246'} 
{> In mutfig at 516} 
Generating output file CTNNB1.stick_fig.jpg
Done
2020-06-19 12:33:28 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.481
Processing input file /cromwell_root/CTNNB1.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 BCL9. {ECO:0000269|PubMed:1705246'} 
{> In mutfig at 516} 
Generating output file CTNNB1.stick_fig.pdf
Done
2020-06-19 12:33:28 AM::INFO  Working with gene: JAK1
2020-06-19 12:33:35 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.497
Processing input file /cromwell_root/JAK1.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 JAK1.stick_fig.jpg
Done
2020-06-19 12:33:43 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.513
Processing input file /cromwell_root/JAK1.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 JAK1.stick_fig.pdf
Done
2020-06-19 12:33:43 AM::INFO  Working with gene: RNF43
2020-06-19 12:33:49 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.529
Processing input file /cromwell_root/RNF43.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 RNF43.stick_fig.jpg
Done
2020-06-19 12:33:56 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.545
Processing input file /cromwell_root/RNF43.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 RNF43.stick_fig.pdf
Done
2020-06-19 12:33:56 AM::INFO  Working with gene: ZFHX3
2020-06-19 12:34:03 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.561
Processing input file /cromwell_root/ZFHX3.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:
'Homeobox 1. {ECO:0000255|PROSITE- ProRule:PRU00108'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Homeobox 2. {ECO:0000255|PROSITE- ProRule:PRU00108'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Homeobox 3. {ECO:0000255|PROSITE- ProRule:PRU00108'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Homeobox 4. {ECO:0000255|PROSITE- ProRule:PRU00108'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Nuclear localization signal. {ECO:0000269|PubMed:2'} 
{> In mutfig at 516} 
Generating output file ZFHX3.stick_fig.jpg
Done
2020-06-19 12:34:12 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.577
Processing input file /cromwell_root/ZFHX3.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:
'Homeobox 1. {ECO:0000255|PROSITE- ProRule:PRU00108'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Homeobox 2. {ECO:0000255|PROSITE- ProRule:PRU00108'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Homeobox 3. {ECO:0000255|PROSITE- ProRule:PRU00108'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Homeobox 4. {ECO:0000255|PROSITE- ProRule:PRU00108'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Nuclear localization signal. {ECO:0000269|PubMed:2'} 
{> In mutfig at 516} 
Generating output file ZFHX3.stick_fig.pdf
Done
2020-06-19 12:34:12 AM::INFO  Working with gene: RPL5
2020-06-19 12:34:19 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.593
Processing input file /cromwell_root/RPL5.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 RPL5.stick_fig.jpg
Done
2020-06-19 12:34:26 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.609
Processing input file /cromwell_root/RPL5.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 RPL5.stick_fig.pdf
Done
2020-06-19 12:34:26 AM::INFO  Working with gene: CUL3
2020-06-19 12:34:33 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.625
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
2020-06-19 12:34:40 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.641
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
2020-06-19 12:34:40 AM::INFO  Working with gene: NSD1
2020-06-19 12:34:48 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.657
Processing input file /cromwell_root/NSD1.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 NSD1.stick_fig.jpg
Done
2020-06-19 12:34:55 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.673
Processing input file /cromwell_root/NSD1.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 NSD1.stick_fig.pdf
Done
2020-06-19 12:34:55 AM::INFO  Working with gene: GLI1
2020-06-19 12:35:02 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.689
Processing input file /cromwell_root/GLI1.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 SUFU. {ECO:0000269|PubMed:2421734'} 
{> In mutfig at 516} 
Generating output file GLI1.stick_fig.jpg
Done
2020-06-19 12:35:09 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.705
Processing input file /cromwell_root/GLI1.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 SUFU. {ECO:0000269|PubMed:2421734'} 
{> In mutfig at 516} 
Generating output file GLI1.stick_fig.pdf
Done
2020-06-19 12:35:09 AM::INFO  Working with gene: FBXW7
2020-06-19 12:35:18 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.721
Processing input file /cromwell_root/FBXW7.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 FBXW7.stick_fig.jpg
Done
2020-06-19 12:35:27 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.737
Processing input file /cromwell_root/FBXW7.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 FBXW7.stick_fig.pdf
Done
2020-06-19 12:35:27 AM::INFO  Working with gene: NOTCH1
2020-06-19 12:35:34 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.753
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
2020-06-19 12:35:41 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.769
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
2020-06-19 12:35:41 AM::INFO  Working with gene: PPM1D
2020-06-19 12:35:49 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.785
Processing input file /cromwell_root/PPM1D.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 CHEK1. {ECO:0000269|PubMed:158702'} 
{> In mutfig at 516} 
Generating output file PPM1D.stick_fig.jpg
Done
2020-06-19 12:35:55 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.801
Processing input file /cromwell_root/PPM1D.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 CHEK1. {ECO:0000269|PubMed:158702'} 
{> In mutfig at 516} 
Generating output file PPM1D.stick_fig.pdf
Done
2020-06-19 12:35:55 AM::INFO  Working with gene: EIF1AX
2020-06-19 12:36:02 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.817
Processing input file /cromwell_root/EIF1AX.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 EIF1AX.stick_fig.jpg
Done
2020-06-19 12:36:09 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.833
Processing input file /cromwell_root/EIF1AX.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 EIF1AX.stick_fig.pdf
Done
2020-06-19 12:36:09 AM::INFO  Working with gene: NFE2L2
2020-06-19 12:36:16 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.849
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
2020-06-19 12:36:25 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.865
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
2020-06-19 12:36:25 AM::INFO  Working with gene: XPO1
2020-06-19 12:36:33 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.881
Processing input file /cromwell_root/XPO1.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 XPO1.stick_fig.jpg
Done
2020-06-19 12:36:40 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.897
Processing input file /cromwell_root/XPO1.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 XPO1.stick_fig.pdf
Done
2020-06-19 12:36:40 AM::INFO  Working with gene: FGFR4
2020-06-19 12:36:47 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.913
Processing input file /cromwell_root/FGFR4.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 FGFR4.stick_fig.jpg
Done
2020-06-19 12:36:55 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.929
Processing input file /cromwell_root/FGFR4.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 FGFR4.stick_fig.pdf
Done
2020-06-19 12:36:55 AM::INFO  Working with gene: TFRC
2020-06-19 12:37:02 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.945
Processing input file /cromwell_root/TFRC.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:
'Mediates interaction with SH3BP4. {ECO:0000269|Pub'} 
{> In mutfig at 516} 
Generating output file TFRC.stick_fig.jpg
Done
2020-06-19 12:37:09 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.961
Processing input file /cromwell_root/TFRC.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:
'Mediates interaction with SH3BP4. {ECO:0000269|Pub'} 
{> In mutfig at 516} 
Generating output file TFRC.stick_fig.pdf
Done
2020-06-19 12:37:09 AM::INFO  Working with gene: TCEA1
2020-06-19 12:37:15 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.977
Processing input file /cromwell_root/TCEA1.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 TCEA1.stick_fig.jpg
Done
2020-06-19 12:37:22 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.993
Processing input file /cromwell_root/TCEA1.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 TCEA1.stick_fig.pdf
Done
2020-06-19 12:37:22 AM::INFO  Working with gene: BCORL1
2020-06-19 12:37:33 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.1009
Processing input file /cromwell_root/BCORL1.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 BCORL1.stick_fig.jpg
Done
2020-06-19 12:37:40 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.1025
Processing input file /cromwell_root/BCORL1.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 BCORL1.stick_fig.pdf
Done
2020-06-19 12:37:40 AM::INFO  Working with gene: CHD4
2020-06-19 12:37:47 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.1041
Processing input file /cromwell_root/CHD4.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 PCNT. {ECO:0000269|P'} 
{> In mutfig at 516} 
Generating output file CHD4.stick_fig.jpg
Done
2020-06-19 12:37:54 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.1057
Processing input file /cromwell_root/CHD4.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 PCNT. {ECO:0000269|P'} 
{> In mutfig at 516} 
Generating output file CHD4.stick_fig.pdf
Done
2020-06-19 12:37:54 AM::INFO  Working with gene: BTK
2020-06-19 12:38:02 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.1073
Processing input file /cromwell_root/BTK.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 BTK.stick_fig.jpg
Done
2020-06-19 12:38:09 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.1089
Processing input file /cromwell_root/BTK.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 BTK.stick_fig.pdf
Done
2020-06-19 12:38:09 AM::INFO  Working with gene: PDGFRA
2020-06-19 12:38:16 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.1105
Processing input file /cromwell_root/PDGFRA.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 PDGFRA.stick_fig.jpg
Done
2020-06-19 12:38:23 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.1121
Processing input file /cromwell_root/PDGFRA.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 PDGFRA.stick_fig.pdf
Done
2020-06-19 12:38:23 AM::INFO  Working with gene: CLP1
2020-06-19 12:38:30 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.1137
Processing input file /cromwell_root/CLP1.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 CLP1.stick_fig.jpg
Done
2020-06-19 12:38:40 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.1153
Processing input file /cromwell_root/CLP1.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 CLP1.stick_fig.pdf
Done
2020-06-19 12:38:40 AM::INFO  Working with gene: SETD1B
2020-06-19 12:38:47 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.1169
Processing input file /cromwell_root/SETD1B.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 SETD1B.stick_fig.jpg
Done
2020-06-19 12:38:54 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.1185
Processing input file /cromwell_root/SETD1B.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 SETD1B.stick_fig.pdf
Done
2020-06-19 12:38:54 AM::INFO  Working with gene: ARHGAP5
2020-06-19 12:39:00 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.1201
Processing input file /cromwell_root/ARHGAP5.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 ARHGAP5.stick_fig.jpg
Done
2020-06-19 12:39:07 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.1217
Processing input file /cromwell_root/ARHGAP5.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 ARHGAP5.stick_fig.pdf
Done
2020-06-19 12:39:07 AM::INFO  Working with gene: IKZF1
2020-06-19 12:39:14 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.1233
Processing input file /cromwell_root/IKZF1.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 IKZF1.stick_fig.jpg
Done
2020-06-19 12:39:21 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.1249
Processing input file /cromwell_root/IKZF1.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 IKZF1.stick_fig.pdf
Done
2020-06-19 12:39:21 AM::INFO  Working with gene: P2RY8
2020-06-19 12:39:28 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.1265
Processing input file /cromwell_root/P2RY8.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 P2RY8.stick_fig.jpg
Done
2020-06-19 12:39:37 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.1281
Processing input file /cromwell_root/P2RY8.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 P2RY8.stick_fig.pdf
Done
2020-06-19 12:39:37 AM::INFO  Working with gene: IL21R
2020-06-19 12:39:44 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.1297
Processing input file /cromwell_root/IL21R.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 IL21R.stick_fig.jpg
Done
2020-06-19 12:39:51 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.1313
Processing input file /cromwell_root/IL21R.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 IL21R.stick_fig.pdf
Done
2020-06-19 12:39:51 AM::INFO  Working with gene: IDH1
2020-06-19 12:39:58 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.1329
Processing input file /cromwell_root/IDH1.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 IDH1.stick_fig.jpg
Done
2020-06-19 12:40:04 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.1345
Processing input file /cromwell_root/IDH1.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 IDH1.stick_fig.pdf
Done
2020-06-19 12:40:04 AM::INFO  Working with gene: ATM
2020-06-19 12:40:12 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.1361
Processing input file /cromwell_root/ATM.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 ABL1. {ECO:0000269|PubMed:9168117'} 
{> In mutfig at 516} 
Generating output file ATM.stick_fig.jpg
Done
2020-06-19 12:40:19 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.1377
Processing input file /cromwell_root/ATM.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 ABL1. {ECO:0000269|PubMed:9168117'} 
{> In mutfig at 516} 
Generating output file ATM.stick_fig.pdf
Done
2020-06-19 12:40:19 AM::INFO  Working with gene: FLT3
2020-06-19 12:40:26 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.1393
Processing input file /cromwell_root/FLT3.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 FLT3.stick_fig.jpg
Done
2020-06-19 12:40:33 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.1409
Processing input file /cromwell_root/FLT3.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 FLT3.stick_fig.pdf
Done
2020-06-19 12:40:33 AM::INFO  Working with gene: GPC5
2020-06-19 12:40:44 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.1425
Processing input file /cromwell_root/GPC5.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 GPC5.stick_fig.jpg
Done
2020-06-19 12:40:51 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.1441
Processing input file /cromwell_root/GPC5.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 GPC5.stick_fig.pdf
Done
2020-06-19 12:40:51 AM::INFO  Working with gene: FUBP1
2020-06-19 12:40:57 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.1457
Processing input file /cromwell_root/FUBP1.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 FUBP1.stick_fig.jpg
Done
2020-06-19 12:41:04 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.1473
Processing input file /cromwell_root/FUBP1.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 FUBP1.stick_fig.pdf
Done
2020-06-19 12:41:04 AM::INFO  Working with gene: ZMYM2
2020-06-19 12:41:11 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.1489
Processing input file /cromwell_root/ZMYM2.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 ZMYM2.stick_fig.jpg
Done
2020-06-19 12:41:19 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.1505
Processing input file /cromwell_root/ZMYM2.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 ZMYM2.stick_fig.pdf
Done
2020-06-19 12:41:19 AM::INFO  Working with gene: RABEP1
2020-06-19 12:41:26 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.1521
Processing input file /cromwell_root/RABEP1.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 RABEP1.stick_fig.jpg
Done
2020-06-19 12:41:33 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.1537
Processing input file /cromwell_root/RABEP1.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 RABEP1.stick_fig.pdf
Done
2020-06-19 12:41:33 AM::INFO  Working with gene: APC
2020-06-19 12:41:40 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.1553
Processing input file /cromwell_root/APC.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 APC.stick_fig.jpg
Done
2020-06-19 12:41:51 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.1569
Processing input file /cromwell_root/APC.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 APC.stick_fig.pdf
Done
2020-06-19 12:41:51 AM::INFO  Working with gene: BMP5
2020-06-19 12:41:58 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.1585
Processing input file /cromwell_root/BMP5.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 BMP5.stick_fig.jpg
Done
2020-06-19 12:42:05 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.1601
Processing input file /cromwell_root/BMP5.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 BMP5.stick_fig.pdf
Done
2020-06-19 12:42:05 AM::INFO  Working with gene: CANT1
2020-06-19 12:42:11 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.1617
Processing input file /cromwell_root/CANT1.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 CANT1.stick_fig.jpg
Done
2020-06-19 12:42:18 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.1633
Processing input file /cromwell_root/CANT1.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 CANT1.stick_fig.pdf
Done
2020-06-19 12:42:18 AM::INFO  Working with gene: BRAF
2020-06-19 12:42:26 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.1649
Processing input file /cromwell_root/BRAF.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 BRAF.stick_fig.jpg
Done
2020-06-19 12:42:33 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.1665
Processing input file /cromwell_root/BRAF.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 BRAF.stick_fig.pdf
Done
2020-06-19 12:42:33 AM::INFO  Working with gene: LEF1
2020-06-19 12:42:39 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.1681
Processing input file /cromwell_root/LEF1.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 LEF1.stick_fig.jpg
Done
2020-06-19 12:42:46 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.1697
Processing input file /cromwell_root/LEF1.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 LEF1.stick_fig.pdf
Done
2020-06-19 12:42:46 AM::INFO  Working with gene: N4BP2
2020-06-19 12:42:57 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.1713
Processing input file /cromwell_root/N4BP2.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 N4BP2.stick_fig.jpg
Done
2020-06-19 12:43:04 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.1729
Processing input file /cromwell_root/N4BP2.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 N4BP2.stick_fig.pdf
Done
2020-06-19 12:43:04 AM::INFO  Working with gene: ARID1B
2020-06-19 12:43:11 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.1745
Processing input file /cromwell_root/ARID1B.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:0000250|UniProtK'} 
{> In mutfig at 516} 
Generating output file ARID1B.stick_fig.jpg
Done
2020-06-19 12:43:18 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.1761
Processing input file /cromwell_root/ARID1B.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:0000250|UniProtK'} 
{> In mutfig at 516} 
Generating output file ARID1B.stick_fig.pdf
Done
2020-06-19 12:43:18 AM::INFO  Working with gene: SLC34A2
2020-06-19 12:43:25 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.1777
Processing input file /cromwell_root/SLC34A2.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 SLC34A2.stick_fig.jpg
Done
2020-06-19 12:43:32 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.1793
Processing input file /cromwell_root/SLC34A2.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 SLC34A2.stick_fig.pdf
Done
2020-06-19 12:43:32 AM::INFO  Runtime: 14.1776015798 minutes
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.6780da85/err.6
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.6780da85/out.6
  adding: CHD4.stick_fig.pdf (deflated 24%)
  adding: ARID1B.stick_fig.pdf (deflated 24%)
  adding: CTCF.stick_fig.pdf (deflated 23%)
  adding: ZMYM2.stick_fig.pdf (deflated 28%)
  adding: LEF1.stick_fig.pdf (deflated 34%)
  adding: EIF1AX.stick_fig.txt (deflated 61%)
  adding: GPC5.stick_fig.txt (deflated 67%)
  adding: P2RY8.stick_fig.pdf (deflated 30%)
  adding: RB1.stick_fig.pdf (deflated 22%)
  adding: TP53.stick_fig.txt (deflated 87%)
  adding: CTCF.stick_fig.txt (deflated 78%)
  adding: SETD1B.stick_fig.jpg (deflated 20%)
  adding: XPO1.stick_fig.pdf (deflated 31%)
  adding: IKZF1.stick_fig.pdf (deflated 31%)
  adding: CLP1.stick_fig.pdf (deflated 35%)
  adding: P2RY8.stick_fig.txt (deflated 72%)
  adding: KMT2D.stick_fig.jpg (deflated 11%)
  adding: JAK1.stick_fig.txt (deflated 76%)
  adding: TFRC.stick_fig.pdf (deflated 30%)
  adding: CDKN2A.stick_fig.jpg (deflated 22%)
  adding: STK11.stick_fig.jpg (deflated 18%)
  adding: CTNNB1.stick_fig.jpg (deflated 19%)
  adding: KRAS.stick_fig.txt (deflated 92%)
  adding: ZMYM2.stick_fig.jpg (deflated 24%)
  adding: CTCF.stick_fig.jpg (deflated 21%)
  adding: GLI1.stick_fig.txt (deflated 75%)
  adding: EGFR.stick_fig.txt (deflated 87%)
  adding: SLC34A2.stick_fig.pdf (deflated 30%)
  adding: IDH1.stick_fig.jpg (deflated 29%)
  adding: ARHGAP5.stick_fig.jpg (deflated 28%)
  adding: FBXW7.stick_fig.pdf (deflated 25%)
  adding: stderr (stored 0%)
  adding: KEAP1.stick_fig.pdf (deflated 23%)
  adding: ATM.stick_fig.pdf (deflated 21%)
  adding: BMP5.stick_fig.jpg (deflated 33%)
  adding: FLT3.stick_fig.txt (deflated 69%)
  adding: FGFR4.stick_fig.jpg (deflated 30%)
  adding: P2RY8.stick_fig.jpg (deflated 31%)
  adding: ZFHX3.stick_fig.jpg (deflated 12%)
  adding: RNF43.stick_fig.pdf (deflated 31%)
  adding: RABEP1.stick_fig.pdf (deflated 31%)
  adding: RPL22.stick_fig.jpg (deflated 41%)
  adding: PDGFRA.stick_fig.pdf (deflated 24%)
  adding: RPL22.stick_fig.pdf (deflated 37%)
  adding: PIK3CA.stick_fig.jpg (deflated 40%)
  adding: CUL3.stick_fig.pdf (deflated 27%)
  adding: ATM.stick_fig.jpg (deflated 16%)
  adding: PPM1D.stick_fig.pdf (deflated 32%)
  adding: EIF1AX.stick_fig.jpg (deflated 46%)
  adding: SLC34A2.stick_fig.jpg (deflated 33%)
  adding: RB1.stick_fig.jpg (deflated 12%)
  adding: IL21R.stick_fig.jpg (deflated 31%)
  adding: NFE2L2.stick_fig.pdf (deflated 26%)
  adding: FBXW7.stick_fig.txt (deflated 79%)
  adding: PDGFRA.stick_fig.txt (deflated 74%)
  adding: FUBP1.stick_fig.pdf (deflated 34%)
  adding: STK11.stick_fig.pdf (deflated 25%)
  adding: RPL5.stick_fig.jpg (deflated 32%)
  adding: PPM1D.stick_fig.jpg (deflated 30%)
  adding: N4BP2.stick_fig.pdf (deflated 29%)
  adding: ARHGAP5.stick_fig.txt (deflated 74%)
  adding: RPL5.stick_fig.pdf (deflated 32%)
  adding: PTEN.stick_fig.pdf (deflated 12%)
  adding: NSD1.stick_fig.pdf (deflated 23%)
  adding: PPM1D.stick_fig.txt (deflated 66%)
  adding: JAK1.stick_fig.jpg (deflated 27%)
  adding: ARID1A.stick_fig.txt (deflated 81%)
  adding: PIK3CA.stick_fig.txt (deflated 89%)
  adding: ZMYM2.stick_fig.txt (deflated 71%)
  adding: KRAS.stick_fig.pdf (deflated 21%)
  adding: BCORL1.stick_fig.pdf (deflated 24%)
  adding: TCEA1.stick_fig.jpg (deflated 38%)
  adding: TFRC.stick_fig.jpg (deflated 21%)
  adding: SLC34A2.stick_fig.txt (deflated 64%)
  adding: ARID1B.stick_fig.jpg (deflated 16%)
  adding: ZFHX3.stick_fig.pdf (deflated 20%)
  adding: LEF1.stick_fig.jpg (deflated 31%)
  adding: CDKN2A.stick_fig.txt (deflated 71%)
  adding: BMP5.stick_fig.txt (deflated 66%)
  adding: RNF43.stick_fig.txt (deflated 74%)
  adding: FUBP1.stick_fig.txt (deflated 61%)
  adding: CLP1.stick_fig.txt (deflated 59%)
  adding: TP53.stick_fig.jpg (deflated 12%)
  adding: APC.stick_fig.txt (deflated 76%)
  adding: EGFR.stick_fig.jpg (deflated 35%)
  adding: PIK3CA.stick_fig.pdf (deflated 16%)
  adding: gcs_localization.sh (deflated 79%)
  adding: NFE2L2.stick_fig.jpg (deflated 19%)
  adding: EGFR.stick_fig.pdf (deflated 19%)
  adding: CHD4.stick_fig.jpg (deflated 16%)
  adding: NOTCH1.stick_fig.pdf (deflated 21%)
  adding: JAK1.stick_fig.pdf (deflated 29%)
  adding: NF1.stick_fig.txt (deflated 79%)
  adding: NF1.stick_fig.pdf (deflated 17%)
  adding: STK11.stick_fig.txt (deflated 70%)
  adding: N4BP2.stick_fig.jpg (deflated 28%)
  adding: KMT2D.stick_fig.pdf (deflated 17%)
  adding: CLP1.stick_fig.jpg (deflated 41%)
  adding: GLI1.stick_fig.jpg (deflated 17%)
  adding: gcs_transfer.sh (deflated 74%)
  adding: ARHGAP5.stick_fig.pdf (deflated 28%)
  adding: BRAF.stick_fig.txt (deflated 73%)
  adding: FBXW7.stick_fig.jpg (deflated 24%)
  adding: APC.stick_fig.pdf (deflated 21%)
  adding: ARID1A.stick_fig.jpg (deflated 14%)
  adding: BTK.stick_fig.jpg (deflated 21%)
  adding: RB1.stick_fig.txt (deflated 73%)
  adding: IL21R.stick_fig.txt (deflated 66%)
  adding: RNF43.stick_fig.jpg (deflated 30%)
  adding: CUL3.stick_fig.txt (deflated 71%)
  adding: BRAF.stick_fig.jpg (deflated 28%)
  adding: TP53.stick_fig.pdf (deflated 11%)
  adding: NSD1.stick_fig.jpg (deflated 16%)
  adding: IKZF1.stick_fig.jpg (deflated 26%)
  adding: ZFHX3.stick_fig.txt (deflated 78%)
  adding: KMT2D.stick_fig.txt (deflated 78%)
  adding: TCEA1.stick_fig.pdf (deflated 34%)
  adding: GLI1.stick_fig.pdf (deflated 24%)
  adding: NF1.stick_fig.jpg (deflated 12%)
  adding: ARID1B.stick_fig.txt (deflated 72%)
  adding: XPO1.stick_fig.jpg (deflated 21%)
  adding: BTK.stick_fig.pdf (deflated 28%)
  adding: KRAS.stick_fig.jpg (deflated 26%)
  adding: TCEA1.stick_fig.txt (deflated 54%)
  adding: KEAP1.stick_fig.jpg (deflated 18%)
  adding: IL21R.stick_fig.pdf (deflated 31%)
  adding: script (deflated 75%)
  adding: GPC5.stick_fig.pdf (deflated 34%)
  adding: generatedStickFigurePaths.txt (deflated 78%)
  adding: XPO1.stick_fig.txt (deflated 67%)
  adding: APC.stick_fig.jpg (deflated 15%)
  adding: RABEP1.stick_fig.txt (deflated 70%)
  adding: N4BP2.stick_fig.txt (deflated 66%)
  adding: NSD1.stick_fig.txt (deflated 77%)
  adding: NOTCH1.stick_fig.jpg (deflated 13%)
  adding: CUL3.stick_fig.jpg (deflated 23%)
  adding: RPL5.stick_fig.txt (deflated 60%)
  adding: TFRC.stick_fig.txt (deflated 62%)
  adding: SETD1B.stick_fig.txt (deflated 74%)
  adding: IDH1.stick_fig.txt (deflated 70%)
  adding: BMP5.stick_fig.pdf (deflated 32%)
  adding: SETD1B.stick_fig.pdf (deflated 25%)
  adding: IKZF1.stick_fig.txt (deflated 72%)
  adding: PDGFRA.stick_fig.jpg (deflated 18%)
  adding: RPL22.stick_fig.txt (deflated 79%)
  adding: stdout