2020-06-19 01:32:37 PM::INFO  Working with gene: TP53
2020-06-19 01:32:50 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:32:57 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:32:57 PM::INFO  Working with gene: PTEN
2020-06-19 01:33:04 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:33:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:33:11 PM::INFO  Working with gene: ARID1A
2020-06-19 01:33:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:33:26 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:33:26 PM::INFO  Working with gene: CTCF
2020-06-19 01:33:33 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:33:40 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.129
Processing input file /cromwell_root/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 01:33:40 PM::INFO  Working with gene: KRAS
2020-06-19 01:33:46 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.145
Processing input file /cromwell_root/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 01:33:53 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.161
Processing input file /cromwell_root/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 01:33:53 PM::INFO  Working with gene: EGFR
2020-06-19 01:33:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.177
Processing input file /cromwell_root/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 01:34:06 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.193
Processing input file /cromwell_root/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 01:34:06 PM::INFO  Working with gene: KMT2D
2020-06-19 01:34:13 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.209
Processing input file /cromwell_root/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 01:34:20 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.225
Processing input file /cromwell_root/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 01:34:20 PM::INFO  Working with gene: NF1
2020-06-19 01:34:28 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:34:35 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:34:35 PM::INFO  Working with gene: RPL22
2020-06-19 01:34:41 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:34:47 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.289
Processing input file /cromwell_root/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 01:34:47 PM::INFO  Working with gene: STK11
2020-06-19 01:34:54 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.305
Processing input file /cromwell_root/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 01:35:00 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:35:00 PM::INFO  Working with gene: RB1
2020-06-19 01:35:06 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.337
Processing input file /cromwell_root/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 01:35:13 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.353
Processing input file /cromwell_root/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 01:35:13 PM::INFO  Working with gene: CDKN2A
2020-06-19 01:35:19 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:35:25 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.385
Processing input file /cromwell_root/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 01:35:25 PM::INFO  Working with gene: PIK3CA
2020-06-19 01:35:33 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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 01:35:39 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.417
Processing input file /cromwell_root/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 01:35:39 PM::INFO  Working with gene: INPPL1
2020-06-19 01:35:46 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.433
Processing input file /cromwell_root/INPPL1.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 INPPL1.stick_fig.jpg
Done
2020-06-19 01:35:52 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.449
Processing input file /cromwell_root/INPPL1.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 INPPL1.stick_fig.pdf
Done
2020-06-19 01:35:52 PM::INFO  Working with gene: KEAP1
2020-06-19 01:35:58 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.465
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 01:36:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.481
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 01:36:05 PM::INFO  Working with gene: EGFL6
2020-06-19 01:36:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.497
Processing input file /cromwell_root/EGFL6.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 EGFL6.stick_fig.jpg
Done
2020-06-19 01:36:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.513
Processing input file /cromwell_root/EGFL6.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 EGFL6.stick_fig.pdf
Done
2020-06-19 01:36:18 PM::INFO  Working with gene: CTNNB1
2020-06-19 01:36:24 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.529
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 01:36:33 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.545
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 01:36:33 PM::INFO  Working with gene: JAK1
2020-06-19 01:36:39 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.561
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 01:36:45 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.577
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 01:36:45 PM::INFO  Working with gene: RNF43
2020-06-19 01:36:53 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.593
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 01:36:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.609
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 01:36:59 PM::INFO  Working with gene: LMAN1
2020-06-19 01:37:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.625
Processing input file /cromwell_root/LMAN1.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:
'Carbohydrate binding. {ECO:0000255|PROSITE-ProRule'} 
{> In mutfig at 516} 
Generating output file LMAN1.stick_fig.jpg
Done
2020-06-19 01:37:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.641
Processing input file /cromwell_root/LMAN1.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:
'Carbohydrate binding. {ECO:0000255|PROSITE-ProRule'} 
{> In mutfig at 516} 
Generating output file LMAN1.stick_fig.pdf
Done
2020-06-19 01:37:11 PM::INFO  Working with gene: ZFHX3
2020-06-19 01:37:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.657
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 01:37:25 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.673
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 01:37:25 PM::INFO  Working with gene: ARID5B
2020-06-19 01:37:32 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.689
Processing input file /cromwell_root/ARID5B.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 ARID5B.stick_fig.jpg
Done
2020-06-19 01:37:39 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.705
Processing input file /cromwell_root/ARID5B.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 ARID5B.stick_fig.pdf
Done
2020-06-19 01:37:39 PM::INFO  Working with gene: USP13
2020-06-19 01:37:46 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.721
Processing input file /cromwell_root/USP13.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file USP13.stick_fig.jpg
Done
2020-06-19 01:37:52 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.737
Processing input file /cromwell_root/USP13.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file USP13.stick_fig.pdf
Done
2020-06-19 01:37:52 PM::INFO  Working with gene: GPR174
2020-06-19 01:37:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.753
Processing input file /cromwell_root/GPR174.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 GPR174.stick_fig.jpg
Done
2020-06-19 01:38:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.769
Processing input file /cromwell_root/GPR174.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 GPR174.stick_fig.pdf
Done
2020-06-19 01:38:05 PM::INFO  Working with gene: WDR47
2020-06-19 01:38:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.785
Processing input file /cromwell_root/WDR47.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 WDR47.stick_fig.jpg
Done
2020-06-19 01:38:17 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.801
Processing input file /cromwell_root/WDR47.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 WDR47.stick_fig.pdf
Done
2020-06-19 01:38:17 PM::INFO  Working with gene: CR2
2020-06-19 01:38:24 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.817
Processing input file /cromwell_root/CR2.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 CR2.stick_fig.jpg
Done
2020-06-19 01:38:30 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.833
Processing input file /cromwell_root/CR2.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 CR2.stick_fig.pdf
Done
2020-06-19 01:38:30 PM::INFO  Working with gene: PDZD4
2020-06-19 01:38:39 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.849
Processing input file /cromwell_root/PDZD4.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 PDZD4.stick_fig.jpg
Done
2020-06-19 01:38:45 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.865
Processing input file /cromwell_root/PDZD4.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 PDZD4.stick_fig.pdf
Done
2020-06-19 01:38:45 PM::INFO  Working with gene: PZP
2020-06-19 01:38:51 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.881
Processing input file /cromwell_root/PZP.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 PZP.stick_fig.jpg
Done
2020-06-19 01:38:58 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.897
Processing input file /cromwell_root/PZP.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 PZP.stick_fig.pdf
Done
2020-06-19 01:38:58 PM::INFO  Working with gene: ZNF800
2020-06-19 01:39:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.913
Processing input file /cromwell_root/ZNF800.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 ZNF800.stick_fig.jpg
Done
2020-06-19 01:39:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.929
Processing input file /cromwell_root/ZNF800.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 ZNF800.stick_fig.pdf
Done
2020-06-19 01:39:11 PM::INFO  Working with gene: SAMD7
2020-06-19 01:39:17 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.945
Processing input file /cromwell_root/SAMD7.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 SAMD7.stick_fig.jpg
Done
2020-06-19 01:39:23 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.961
Processing input file /cromwell_root/SAMD7.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 SAMD7.stick_fig.pdf
Done
2020-06-19 01:39:23 PM::INFO  Working with gene: ESRP1
2020-06-19 01:39:31 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.977
Processing input file /cromwell_root/ESRP1.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 ESRP1.stick_fig.jpg
Done
2020-06-19 01:39:37 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.993
Processing input file /cromwell_root/ESRP1.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 ESRP1.stick_fig.pdf
Done
2020-06-19 01:39:37 PM::INFO  Working with gene: RPL5
2020-06-19 01:39:45 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1009
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 01:39:51 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1025
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 01:39:51 PM::INFO  Working with gene: UCHL5
2020-06-19 01:39:58 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1041
Processing input file /cromwell_root/UCHL5.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 UCHL5.stick_fig.jpg
Done
2020-06-19 01:40:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1057
Processing input file /cromwell_root/UCHL5.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 UCHL5.stick_fig.pdf
Done
2020-06-19 01:40:05 PM::INFO  Working with gene: CUL3
2020-06-19 01:40:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1073
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 01:40:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1089
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 01:40:18 PM::INFO  Working with gene: NSD1
2020-06-19 01:40:24 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1105
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 01:40:30 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1121
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 01:40:30 PM::INFO  Working with gene: MBD1
2020-06-19 01:40:38 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1137
Processing input file /cromwell_root/MBD1.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 MBD1.stick_fig.jpg
Done
2020-06-19 01:40:46 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1153
Processing input file /cromwell_root/MBD1.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 MBD1.stick_fig.pdf
Done
2020-06-19 01:40:46 PM::INFO  Working with gene: SEC31A
2020-06-19 01:40:53 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1169
Processing input file /cromwell_root/SEC31A.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 SEC13. {ECO:0000269|PubMed:169570'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with PDCD6. {ECO:0000269|PubMed:169570'} 
{> In mutfig at 516} 
Generating output file SEC31A.stick_fig.jpg
Done
2020-06-19 01:40:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1185
Processing input file /cromwell_root/SEC31A.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 SEC13. {ECO:0000269|PubMed:169570'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with PDCD6. {ECO:0000269|PubMed:169570'} 
{> In mutfig at 516} 
Generating output file SEC31A.stick_fig.pdf
Done
2020-06-19 01:40:59 PM::INFO  Working with gene: DFNA5
2020-06-19 01:41:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1201
Processing input file /cromwell_root/DFNA5.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 DFNA5.stick_fig.jpg
Done
2020-06-19 01:41:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1217
Processing input file /cromwell_root/DFNA5.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 DFNA5.stick_fig.pdf
Done
2020-06-19 01:41:11 PM::INFO  Working with gene: FYB
2020-06-19 01:41:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1233
Processing input file /cromwell_root/FYB.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 FYB.stick_fig.jpg
Done
2020-06-19 01:41:24 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1249
Processing input file /cromwell_root/FYB.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 FYB.stick_fig.pdf
Done
2020-06-19 01:41:24 PM::INFO  Working with gene: PYHIN1
2020-06-19 01:41:30 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1265
Processing input file /cromwell_root/PYHIN1.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 PYHIN1.stick_fig.jpg
Done
2020-06-19 01:41:36 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1281
Processing input file /cromwell_root/PYHIN1.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 PYHIN1.stick_fig.pdf
Done
2020-06-19 01:41:36 PM::INFO  Working with gene: TP53BP1
2020-06-19 01:41:42 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1297
Processing input file /cromwell_root/TP53BP1.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 dimethylated histone H4. {ECO:000'} 
{> In mutfig at 516} 
Generating output file TP53BP1.stick_fig.jpg
Done
2020-06-19 01:41:51 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1313
Processing input file /cromwell_root/TP53BP1.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 dimethylated histone H4. {ECO:000'} 
{> In mutfig at 516} 
Generating output file TP53BP1.stick_fig.pdf
Done
2020-06-19 01:41:51 PM::INFO  Working with gene: AL358113.1
2020-06-19 01:41:57 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1329
Processing input file /cromwell_root/AL358113.1.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 SCRIB. {ECO:0000269|PubMed:159755'} 
{> In mutfig at 516} 
Generating output file AL358113.1.stick_fig.jpg
Done
2020-06-19 01:42:04 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1345
Processing input file /cromwell_root/AL358113.1.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 SCRIB. {ECO:0000269|PubMed:159755'} 
{> In mutfig at 516} 
Generating output file AL358113.1.stick_fig.pdf
Done
2020-06-19 01:42:04 PM::INFO  Working with gene: DHX9
2020-06-19 01:42:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1361
Processing input file /cromwell_root/DHX9.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:
'ATP. {ECO:0000244|PDB:3LLM, ECO:0000269|PubMed:114'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with CREBBP. {ECO:0000269|PubMed:93231'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'siRNA-binding. {ECO:0000244|PDB:3VYY, ECO:0000269|'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'siRNA-binding. {ECO:0000244|PDB:3VYX, ECO:0000269|'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with BRCA1. {ECO:0000269|PubMed:966239'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Necessary for interaction with H2AFX. {ECO:0000269'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'OB-fold. {ECO:0000269|PubMed:20696886, ECO:0000269'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'RGG. {ECO:0000269|PubMed:10207077, ECO:0000269|Pub'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Nuclear localization signal (NLS2). {ECO:0000269|P'} 
{> In mutfig at 516} 
Generating output file DHX9.stick_fig.jpg
Done
2020-06-19 01:42:17 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1377
Processing input file /cromwell_root/DHX9.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:
'ATP. {ECO:0000244|PDB:3LLM, ECO:0000269|PubMed:114'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with CREBBP. {ECO:0000269|PubMed:93231'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'siRNA-binding. {ECO:0000244|PDB:3VYY, ECO:0000269|'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'siRNA-binding. {ECO:0000244|PDB:3VYX, ECO:0000269|'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with BRCA1. {ECO:0000269|PubMed:966239'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Necessary for interaction with H2AFX. {ECO:0000269'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'OB-fold. {ECO:0000269|PubMed:20696886, ECO:0000269'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'RGG. {ECO:0000269|PubMed:10207077, ECO:0000269|Pub'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Nuclear localization signal (NLS2). {ECO:0000269|P'} 
{> In mutfig at 516} 
Generating output file DHX9.stick_fig.pdf
Done
2020-06-19 01:42:17 PM::INFO  Working with gene: CYBB
2020-06-19 01:42:24 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1393
Processing input file /cromwell_root/CYBB.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 CYBB.stick_fig.jpg
Done
2020-06-19 01:42:30 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1409
Processing input file /cromwell_root/CYBB.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 CYBB.stick_fig.pdf
Done
2020-06-19 01:42:30 PM::INFO  Working with gene: MEDAG
2020-06-19 01:42:36 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1425
Processing input file /cromwell_root/MEDAG.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 MEDAG.stick_fig.jpg
Done
2020-06-19 01:42:43 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1441
Processing input file /cromwell_root/MEDAG.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 MEDAG.stick_fig.pdf
Done
2020-06-19 01:42:43 PM::INFO  Working with gene: GLI1
2020-06-19 01:42:52 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1457
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 01:42:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1473
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 01:42:59 PM::INFO  Working with gene: SCAF4
2020-06-19 01:43:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1489
Processing input file /cromwell_root/SCAF4.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 SCAF4.stick_fig.jpg
Done
2020-06-19 01:43:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1505
Processing input file /cromwell_root/SCAF4.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 SCAF4.stick_fig.pdf
Done
2020-06-19 01:43:11 PM::INFO  Working with gene: RASA1
2020-06-19 01:43:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1521
Processing input file /cromwell_root/RASA1.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 RASA1.stick_fig.jpg
Done
2020-06-19 01:43:25 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1537
Processing input file /cromwell_root/RASA1.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 RASA1.stick_fig.pdf
Done
2020-06-19 01:43:25 PM::INFO  Working with gene: FBXW7
2020-06-19 01:43:31 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1553
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 01:43:37 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1569
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 01:43:37 PM::INFO  Working with gene: APBB1IP
2020-06-19 01:43:43 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1585
Processing input file /cromwell_root/APBB1IP.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 APBB1IP.stick_fig.jpg
Done
2020-06-19 01:43:51 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1601
Processing input file /cromwell_root/APBB1IP.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 APBB1IP.stick_fig.pdf
Done
2020-06-19 01:43:51 PM::INFO  Working with gene: ARHGAP35
2020-06-19 01:43:58 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1617
Processing input file /cromwell_root/ARHGAP35.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 ARHGAP35.stick_fig.jpg
Done
2020-06-19 01:44:04 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1633
Processing input file /cromwell_root/ARHGAP35.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 ARHGAP35.stick_fig.pdf
Done
2020-06-19 01:44:04 PM::INFO  Working with gene: TMEM202
2020-06-19 01:44:10 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1649
Processing input file /cromwell_root/TMEM202.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 TMEM202.stick_fig.jpg
Done
2020-06-19 01:44:17 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1665
Processing input file /cromwell_root/TMEM202.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 TMEM202.stick_fig.pdf
Done
2020-06-19 01:44:17 PM::INFO  Working with gene: GLRA4
2020-06-19 01:44:23 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1681
Processing input file /cromwell_root/GLRA4.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 GLRA4.stick_fig.jpg
Done
2020-06-19 01:44:29 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1697
Processing input file /cromwell_root/GLRA4.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 GLRA4.stick_fig.pdf
Done
2020-06-19 01:44:29 PM::INFO  Working with gene: RBM27
2020-06-19 01:44:35 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1713
Processing input file /cromwell_root/RBM27.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 RBM27.stick_fig.jpg
Done
2020-06-19 01:44:42 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1729
Processing input file /cromwell_root/RBM27.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 RBM27.stick_fig.pdf
Done
2020-06-19 01:44:42 PM::INFO  Working with gene: TFDP1
2020-06-19 01:44:48 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1745
Processing input file /cromwell_root/TFDP1.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 CEBPA. {ECO:0000269|PubMed:201768'} 
{> In mutfig at 516} 
Generating output file TFDP1.stick_fig.jpg
Done
2020-06-19 01:44:56 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1761
Processing input file /cromwell_root/TFDP1.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 CEBPA. {ECO:0000269|PubMed:201768'} 
{> In mutfig at 516} 
Generating output file TFDP1.stick_fig.pdf
Done
2020-06-19 01:44:56 PM::INFO  Working with gene: TIGIT
2020-06-19 01:45:02 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1777
Processing input file /cromwell_root/TIGIT.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 TIGIT.stick_fig.jpg
Done
2020-06-19 01:45:09 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1793
Processing input file /cromwell_root/TIGIT.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 TIGIT.stick_fig.pdf
Done
2020-06-19 01:45:09 PM::INFO  Working with gene: BSX
2020-06-19 01:45:15 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1809
Processing input file /cromwell_root/BSX.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 BSX.stick_fig.jpg
Done
2020-06-19 01:45:22 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1825
Processing input file /cromwell_root/BSX.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 BSX.stick_fig.pdf
Done
2020-06-19 01:45:22 PM::INFO  Working with gene: MS4A14
2020-06-19 01:45:28 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1841
Processing input file /cromwell_root/MS4A14.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 MS4A14.stick_fig.jpg
Done
2020-06-19 01:45:34 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1857
Processing input file /cromwell_root/MS4A14.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 MS4A14.stick_fig.pdf
Done
2020-06-19 01:45:34 PM::INFO  Working with gene: SPTY2D1
2020-06-19 01:45:40 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1873
Processing input file /cromwell_root/SPTY2D1.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:
'Important for interaction with DNA. {ECO:0000269|P'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Important for interaction with histones. {ECO:0000'} 
{> In mutfig at 516} 
Generating output file SPTY2D1.stick_fig.jpg
Done
2020-06-19 01:45:47 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1889
Processing input file /cromwell_root/SPTY2D1.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:
'Important for interaction with DNA. {ECO:0000269|P'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Important for interaction with histones. {ECO:0000'} 
{> In mutfig at 516} 
Generating output file SPTY2D1.stick_fig.pdf
Done
2020-06-19 01:45:47 PM::INFO  Working with gene: PLXNB2
2020-06-19 01:45:54 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1905
Processing input file /cromwell_root/PLXNB2.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 PLXNB2.stick_fig.jpg
Done
2020-06-19 01:46:02 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1921
Processing input file /cromwell_root/PLXNB2.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 PLXNB2.stick_fig.pdf
Done
2020-06-19 01:46:02 PM::INFO  Working with gene: CHD3
2020-06-19 01:46:09 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1937
Processing input file /cromwell_root/CHD3.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 CHD3.stick_fig.jpg
Done
2020-06-19 01:46:15 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1953
Processing input file /cromwell_root/CHD3.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 CHD3.stick_fig.pdf
Done
2020-06-19 01:46:15 PM::INFO  Working with gene: NOTCH1
2020-06-19 01:46:21 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1969
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 01:46:29 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.1985
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 01:46:29 PM::INFO  Working with gene: WWC3
2020-06-19 01:46:35 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2001
Processing input file /cromwell_root/WWC3.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 WWC3.stick_fig.jpg
Done
2020-06-19 01:46:41 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2017
Processing input file /cromwell_root/WWC3.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 WWC3.stick_fig.pdf
Done
2020-06-19 01:46:41 PM::INFO  Working with gene: PPM1D
2020-06-19 01:46:47 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2033
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 01:46:53 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2049
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 01:46:53 PM::INFO  Working with gene: GRIK3
2020-06-19 01:47:03 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2065
Processing input file /cromwell_root/GRIK3.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 GRIK3.stick_fig.jpg
Done
2020-06-19 01:47:10 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2081
Processing input file /cromwell_root/GRIK3.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 GRIK3.stick_fig.pdf
Done
2020-06-19 01:47:10 PM::INFO  Working with gene: TMEM39A
2020-06-19 01:47:16 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2097
Processing input file /cromwell_root/TMEM39A.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 TMEM39A.stick_fig.jpg
Done
2020-06-19 01:47:22 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2113
Processing input file /cromwell_root/TMEM39A.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 TMEM39A.stick_fig.pdf
Done
2020-06-19 01:47:22 PM::INFO  Working with gene: XPOT
2020-06-19 01:47:28 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2129
Processing input file /cromwell_root/XPOT.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 XPOT.stick_fig.jpg
Done
2020-06-19 01:47:34 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2145
Processing input file /cromwell_root/XPOT.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 XPOT.stick_fig.pdf
Done
2020-06-19 01:47:34 PM::INFO  Working with gene: EIF1AX
2020-06-19 01:47:41 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2161
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 01:47:47 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2177
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 01:47:47 PM::INFO  Working with gene: NEFM
2020-06-19 01:47:53 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2193
Processing input file /cromwell_root/NEFM.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 NEFM.stick_fig.jpg
Done
2020-06-19 01:47:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2209
Processing input file /cromwell_root/NEFM.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 NEFM.stick_fig.pdf
Done
2020-06-19 01:47:59 PM::INFO  Working with gene: CUL4B
2020-06-19 01:48:09 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2225
Processing input file /cromwell_root/CUL4B.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:1'} 
{> In mutfig at 516} 
Generating output file CUL4B.stick_fig.jpg
Done
2020-06-19 01:48:15 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2241
Processing input file /cromwell_root/CUL4B.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:1'} 
{> In mutfig at 516} 
Generating output file CUL4B.stick_fig.pdf
Done
2020-06-19 01:48:15 PM::INFO  Working with gene: JPH3
2020-06-19 01:48:21 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2257
Processing input file /cromwell_root/JPH3.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 JPH3.stick_fig.jpg
Done
2020-06-19 01:48:27 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2273
Processing input file /cromwell_root/JPH3.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 JPH3.stick_fig.pdf
Done
2020-06-19 01:48:27 PM::INFO  Working with gene: ZNF300
2020-06-19 01:48:35 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2289
Processing input file /cromwell_root/ZNF300.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 ZNF300.stick_fig.jpg
Done
2020-06-19 01:48:41 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2305
Processing input file /cromwell_root/ZNF300.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 ZNF300.stick_fig.pdf
Done
2020-06-19 01:48:41 PM::INFO  Working with gene: IFNAR1
2020-06-19 01:48:47 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2321
Processing input file /cromwell_root/IFNAR1.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:
'Important for interaction with TYK2. {ECO:0000269|'} 
{> In mutfig at 516} 
Generating output file IFNAR1.stick_fig.jpg
Done
2020-06-19 01:48:53 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2337
Processing input file /cromwell_root/IFNAR1.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:
'Important for interaction with TYK2. {ECO:0000269|'} 
{> In mutfig at 516} 
Generating output file IFNAR1.stick_fig.pdf
Done
2020-06-19 01:48:53 PM::INFO  Working with gene: SAMD9
2020-06-19 01:49:00 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2353
Processing input file /cromwell_root/SAMD9.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 SAMD9.stick_fig.jpg
Done
2020-06-19 01:49:10 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2369
Processing input file /cromwell_root/SAMD9.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 SAMD9.stick_fig.pdf
Done
2020-06-19 01:49:10 PM::INFO  Working with gene: ADGRE1
2020-06-19 01:49:16 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2385
Processing input file /cromwell_root/ADGRE1.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 ADGRE1.stick_fig.jpg
Done
2020-06-19 01:49:22 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2401
Processing input file /cromwell_root/ADGRE1.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 ADGRE1.stick_fig.pdf
Done
2020-06-19 01:49:22 PM::INFO  Working with gene: RNF2
2020-06-19 01:49:28 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2417
Processing input file /cromwell_root/RNF2.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 HIP2. {ECO:0000269|PubMed:1151385'} 
{> In mutfig at 516} 
Generating output file RNF2.stick_fig.jpg
Done
2020-06-19 01:49:35 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2433
Processing input file /cromwell_root/RNF2.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 HIP2. {ECO:0000269|PubMed:1151385'} 
{> In mutfig at 516} 
Generating output file RNF2.stick_fig.pdf
Done
2020-06-19 01:49:35 PM::INFO  Working with gene: AGO2
2020-06-19 01:49:42 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2449
Processing input file /cromwell_root/AGO2.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 GW182 family members. {ECO:000025'} 
{> In mutfig at 516} 
Generating output file AGO2.stick_fig.jpg
Done
2020-06-19 01:49:48 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2465
Processing input file /cromwell_root/AGO2.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 GW182 family members. {ECO:000025'} 
{> In mutfig at 516} 
Generating output file AGO2.stick_fig.pdf
Done
2020-06-19 01:49:48 PM::INFO  Working with gene: PIGO
2020-06-19 01:49:54 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2481
Processing input file /cromwell_root/PIGO.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 PIGO.stick_fig.jpg
Done
2020-06-19 01:50:01 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2497
Processing input file /cromwell_root/PIGO.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 PIGO.stick_fig.pdf
Done
2020-06-19 01:50:01 PM::INFO  Working with gene: KRIT1
2020-06-19 01:50:07 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2513
Processing input file /cromwell_root/KRIT1.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 RAP1B. {ECO:0000269|PubMed:225771'} 
{> In mutfig at 516} 
Generating output file KRIT1.stick_fig.jpg
Done
2020-06-19 01:50:17 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2529
Processing input file /cromwell_root/KRIT1.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 RAP1B. {ECO:0000269|PubMed:225771'} 
{> In mutfig at 516} 
Generating output file KRIT1.stick_fig.pdf
Done
2020-06-19 01:50:17 PM::INFO  Working with gene: CD300LG
2020-06-19 01:50:23 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2545
Processing input file /cromwell_root/CD300LG.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 CD300LG.stick_fig.jpg
Done
2020-06-19 01:50:29 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2561
Processing input file /cromwell_root/CD300LG.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 CD300LG.stick_fig.pdf
Done
2020-06-19 01:50:29 PM::INFO  Working with gene: KIAA1551
2020-06-19 01:50:35 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2577
Processing input file /cromwell_root/KIAA1551.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 KIAA1551.stick_fig.jpg
Done
2020-06-19 01:50:42 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2593
Processing input file /cromwell_root/KIAA1551.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 KIAA1551.stick_fig.pdf
Done
2020-06-19 01:50:42 PM::INFO  Working with gene: PLEKHA4
2020-06-19 01:50:49 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2609
Processing input file /cromwell_root/PLEKHA4.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 PLEKHA4.stick_fig.jpg
Done
2020-06-19 01:50:55 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2625
Processing input file /cromwell_root/PLEKHA4.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 PLEKHA4.stick_fig.pdf
Done
2020-06-19 01:50:55 PM::INFO  Working with gene: H2AFY2
2020-06-19 01:51:01 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2641
Processing input file /cromwell_root/H2AFY2.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 H2AFY2.stick_fig.jpg
Done
2020-06-19 01:51:08 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2657
Processing input file /cromwell_root/H2AFY2.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 H2AFY2.stick_fig.pdf
Done
2020-06-19 01:51:08 PM::INFO  Working with gene: PRPF6
2020-06-19 01:51:16 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2673
Processing input file /cromwell_root/PRPF6.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 PRPF6.stick_fig.jpg
Done
2020-06-19 01:51:22 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2689
Processing input file /cromwell_root/PRPF6.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 PRPF6.stick_fig.pdf
Done
2020-06-19 01:51:22 PM::INFO  Working with gene: XPO5
2020-06-19 01:51:28 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2705
Processing input file /cromwell_root/XPO5.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 XPO5.stick_fig.jpg
Done
2020-06-19 01:51:35 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2721
Processing input file /cromwell_root/XPO5.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 XPO5.stick_fig.pdf
Done
2020-06-19 01:51:35 PM::INFO  Working with gene: ZFP36L2
2020-06-19 01:51:41 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2737
Processing input file /cromwell_root/ZFP36L2.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:
'RNA-binding. {ECO:0000269|PubMed:14981510, ECO:000'} 
{> In mutfig at 516} 
Generating output file ZFP36L2.stick_fig.jpg
Done
2020-06-19 01:51:47 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2753
Processing input file /cromwell_root/ZFP36L2.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:
'RNA-binding. {ECO:0000269|PubMed:14981510, ECO:000'} 
{> In mutfig at 516} 
Generating output file ZFP36L2.stick_fig.pdf
Done
2020-06-19 01:51:47 PM::INFO  Working with gene: LINGO4
2020-06-19 01:51:53 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2769
Processing input file /cromwell_root/LINGO4.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 LINGO4.stick_fig.jpg
Done
2020-06-19 01:51:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2785
Processing input file /cromwell_root/LINGO4.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 LINGO4.stick_fig.pdf
Done
2020-06-19 01:51:59 PM::INFO  Working with gene: NFE2L2
2020-06-19 01:52:06 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2801
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 01:52:12 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2817
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 01:52:12 PM::INFO  Working with gene: FAM171B
2020-06-19 01:52:22 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2833
Processing input file /cromwell_root/FAM171B.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 FAM171B.stick_fig.jpg
Done
2020-06-19 01:52:28 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2849
Processing input file /cromwell_root/FAM171B.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 FAM171B.stick_fig.pdf
Done
2020-06-19 01:52:28 PM::INFO  Working with gene: AIM1L
2020-06-19 01:52:34 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2865
Processing input file /cromwell_root/AIM1L.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 AIM1L.stick_fig.jpg
Done
2020-06-19 01:52:40 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2881
Processing input file /cromwell_root/AIM1L.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 AIM1L.stick_fig.pdf
Done
2020-06-19 01:52:40 PM::INFO  Working with gene: BNC2
2020-06-19 01:52:47 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2897
Processing input file /cromwell_root/BNC2.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 BNC2.stick_fig.jpg
Done
2020-06-19 01:52:54 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2913
Processing input file /cromwell_root/BNC2.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 BNC2.stick_fig.pdf
Done
2020-06-19 01:52:54 PM::INFO  Working with gene: KRTAP10-4
2020-06-19 01:53:00 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2929
Processing input file /cromwell_root/KRTAP10-4.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 KRTAP10-4.stick_fig.jpg
Done
2020-06-19 01:53:06 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2945
Processing input file /cromwell_root/KRTAP10-4.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 KRTAP10-4.stick_fig.pdf
Done
2020-06-19 01:53:06 PM::INFO  Working with gene: TLR7
2020-06-19 01:53:13 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2961
Processing input file /cromwell_root/TLR7.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 TLR7.stick_fig.jpg
Done
2020-06-19 01:53:19 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2977
Processing input file /cromwell_root/TLR7.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 TLR7.stick_fig.pdf
Done
2020-06-19 01:53:19 PM::INFO  Working with gene: CPZ
2020-06-19 01:53:27 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.2993
Processing input file /cromwell_root/CPZ.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 CPZ.stick_fig.jpg
Done
2020-06-19 01:53:33 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3009
Processing input file /cromwell_root/CPZ.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 CPZ.stick_fig.pdf
Done
2020-06-19 01:53:33 PM::INFO  Working with gene: XPO1
2020-06-19 01:53:39 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3025
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 01:53:45 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3041
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 01:53:45 PM::INFO  Working with gene: OTX1
2020-06-19 01:53:52 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3057
Processing input file /cromwell_root/OTX1.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 OTX1.stick_fig.jpg
Done
2020-06-19 01:53:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3073
Processing input file /cromwell_root/OTX1.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 OTX1.stick_fig.pdf
Done
2020-06-19 01:53:59 PM::INFO  Working with gene: PCDHGA1
2020-06-19 01:54:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3089
Processing input file /cromwell_root/PCDHGA1.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 PCDHGA1.stick_fig.jpg
Done
2020-06-19 01:54:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3105
Processing input file /cromwell_root/PCDHGA1.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 PCDHGA1.stick_fig.pdf
Done
2020-06-19 01:54:11 PM::INFO  Working with gene: LMNB2
2020-06-19 01:54:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3121
Processing input file /cromwell_root/LMNB2.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 LMNB2.stick_fig.jpg
Done
2020-06-19 01:54:26 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3137
Processing input file /cromwell_root/LMNB2.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 LMNB2.stick_fig.pdf
Done
2020-06-19 01:54:26 PM::INFO  Working with gene: CNGA2
2020-06-19 01:54:34 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3153
Processing input file /cromwell_root/CNGA2.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 CNGA2.stick_fig.jpg
Done
2020-06-19 01:54:40 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3169
Processing input file /cromwell_root/CNGA2.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 CNGA2.stick_fig.pdf
Done
2020-06-19 01:54:40 PM::INFO  Working with gene: ERMP1
2020-06-19 01:54:46 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3185
Processing input file /cromwell_root/ERMP1.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 ERMP1.stick_fig.jpg
Done
2020-06-19 01:54:53 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3201
Processing input file /cromwell_root/ERMP1.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 ERMP1.stick_fig.pdf
Done
2020-06-19 01:54:53 PM::INFO  Working with gene: KCNK15
2020-06-19 01:54:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3217
Processing input file /cromwell_root/KCNK15.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 KCNK15.stick_fig.jpg
Done
2020-06-19 01:55:06 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3233
Processing input file /cromwell_root/KCNK15.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 KCNK15.stick_fig.pdf
Done
2020-06-19 01:55:06 PM::INFO  Working with gene: FGFR4
2020-06-19 01:55:13 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3249
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 01:55:19 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3265
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 01:55:19 PM::INFO  Working with gene: RRAS2
2020-06-19 01:55:27 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3281
Processing input file /cromwell_root/RRAS2.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 RRAS2.stick_fig.jpg
Done
2020-06-19 01:55:33 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3297
Processing input file /cromwell_root/RRAS2.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 RRAS2.stick_fig.pdf
Done
2020-06-19 01:55:33 PM::INFO  Working with gene: KMT2B
2020-06-19 01:55:40 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3313
Processing input file /cromwell_root/KMT2B.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 KMT2B.stick_fig.jpg
Done
2020-06-19 01:55:46 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3329
Processing input file /cromwell_root/KMT2B.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 KMT2B.stick_fig.pdf
Done
2020-06-19 01:55:46 PM::INFO  Working with gene: TFRC
2020-06-19 01:55:52 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3345
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 01:55:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3361
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 01:55:59 PM::INFO  Working with gene: DENND2A
2020-06-19 01:56:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3377
Processing input file /cromwell_root/DENND2A.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 DENND2A.stick_fig.jpg
Done
2020-06-19 01:56:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3393
Processing input file /cromwell_root/DENND2A.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 DENND2A.stick_fig.pdf
Done
2020-06-19 01:56:11 PM::INFO  Working with gene: MGA
2020-06-19 01:56:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3409
Processing input file /cromwell_root/MGA.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 MGA.stick_fig.jpg
Done
2020-06-19 01:56:24 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3425
Processing input file /cromwell_root/MGA.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 MGA.stick_fig.pdf
Done
2020-06-19 01:56:24 PM::INFO  Working with gene: CLEC16A
2020-06-19 01:56:33 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3441
Processing input file /cromwell_root/CLEC16A.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 CLEC16A.stick_fig.jpg
Done
2020-06-19 01:56:40 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3457
Processing input file /cromwell_root/CLEC16A.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 CLEC16A.stick_fig.pdf
Done
2020-06-19 01:56:40 PM::INFO  Working with gene: TCEA1
2020-06-19 01:56:46 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3473
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 01:56:53 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3489
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 01:56:53 PM::INFO  Working with gene: ZFP57
2020-06-19 01:56:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3505
Processing input file /cromwell_root/ZFP57.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 ZFP57.stick_fig.jpg
Done
2020-06-19 01:57:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3521
Processing input file /cromwell_root/ZFP57.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 ZFP57.stick_fig.pdf
Done
2020-06-19 01:57:05 PM::INFO  Working with gene: COL4A3BP
2020-06-19 01:57:12 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3537
Processing input file /cromwell_root/COL4A3BP.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 COL4A3BP.stick_fig.jpg
Done
2020-06-19 01:57:19 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3553
Processing input file /cromwell_root/COL4A3BP.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 COL4A3BP.stick_fig.pdf
Done
2020-06-19 01:57:19 PM::INFO  Working with gene: IFNGR1
2020-06-19 01:57:25 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3569
Processing input file /cromwell_root/IFNGR1.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 IFNGR1.stick_fig.jpg
Done
2020-06-19 01:57:33 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3585
Processing input file /cromwell_root/IFNGR1.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 IFNGR1.stick_fig.pdf
Done
2020-06-19 01:57:33 PM::INFO  Working with gene: RAB3IL1
2020-06-19 01:57:40 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3601
Processing input file /cromwell_root/RAB3IL1.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 RAB3IL1.stick_fig.jpg
Done
2020-06-19 01:57:46 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3617
Processing input file /cromwell_root/RAB3IL1.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 RAB3IL1.stick_fig.pdf
Done
2020-06-19 01:57:46 PM::INFO  Working with gene: TSNAX
2020-06-19 01:57:53 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3633
Processing input file /cromwell_root/TSNAX.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 C1D. {ECO:0000269|PubMed:11801738'} 
{> In mutfig at 516} 
Generating output file TSNAX.stick_fig.jpg
Done
2020-06-19 01:57:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3649
Processing input file /cromwell_root/TSNAX.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 C1D. {ECO:0000269|PubMed:11801738'} 
{> In mutfig at 516} 
Generating output file TSNAX.stick_fig.pdf
Done
2020-06-19 01:57:59 PM::INFO  Working with gene: ZNF541
2020-06-19 01:58:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3665
Processing input file /cromwell_root/ZNF541.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 ZNF541.stick_fig.jpg
Done
2020-06-19 01:58:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3681
Processing input file /cromwell_root/ZNF541.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 ZNF541.stick_fig.pdf
Done
2020-06-19 01:58:11 PM::INFO  Working with gene: CLOCK
2020-06-19 01:58:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3697
Processing input file /cromwell_root/CLOCK.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 NR3C1. {ECO:0000250|UniProtKB:O08'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with SIRT1. {ECO:0000250|UniProtKB:O08'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Implicated in the circadian rhythmicity. {ECO:0000'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Nuclear localization signal. {ECO:0000250|UniProtK'} 
{> In mutfig at 516} 
Generating output file CLOCK.stick_fig.jpg
Done
2020-06-19 01:58:25 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3713
Processing input file /cromwell_root/CLOCK.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 NR3C1. {ECO:0000250|UniProtKB:O08'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with SIRT1. {ECO:0000250|UniProtKB:O08'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Implicated in the circadian rhythmicity. {ECO:0000'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Nuclear localization signal. {ECO:0000250|UniProtK'} 
{> In mutfig at 516} 
Generating output file CLOCK.stick_fig.pdf
Done
2020-06-19 01:58:25 PM::INFO  Working with gene: AFM
2020-06-19 01:58:31 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3729
Processing input file /cromwell_root/AFM.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 AFM.stick_fig.jpg
Done
2020-06-19 01:58:38 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3745
Processing input file /cromwell_root/AFM.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 AFM.stick_fig.pdf
Done
2020-06-19 01:58:38 PM::INFO  Working with gene: PUS1
2020-06-19 01:58:45 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3761
Processing input file /cromwell_root/PUS1.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 PUS1.stick_fig.jpg
Done
2020-06-19 01:58:51 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3777
Processing input file /cromwell_root/PUS1.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 PUS1.stick_fig.pdf
Done
2020-06-19 01:58:51 PM::INFO  Working with gene: ZNF853
2020-06-19 01:58:57 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3793
Processing input file /cromwell_root/ZNF853.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 ZNF853.stick_fig.jpg
Done
2020-06-19 01:59:03 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3809
Processing input file /cromwell_root/ZNF853.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 ZNF853.stick_fig.pdf
Done
2020-06-19 01:59:03 PM::INFO  Working with gene: IPO7
2020-06-19 01:59:10 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3825
Processing input file /cromwell_root/IPO7.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 IPO7.stick_fig.jpg
Done
2020-06-19 01:59:16 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3841
Processing input file /cromwell_root/IPO7.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 IPO7.stick_fig.pdf
Done
2020-06-19 01:59:16 PM::INFO  Working with gene: TP53TG5
2020-06-19 01:59:22 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3857
Processing input file /cromwell_root/TP53TG5.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 TP53TG5.stick_fig.jpg
Done
2020-06-19 01:59:28 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3873
Processing input file /cromwell_root/TP53TG5.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 TP53TG5.stick_fig.pdf
Done
2020-06-19 01:59:28 PM::INFO  Working with gene: CT47B1
2020-06-19 01:59:36 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3889
Processing input file /cromwell_root/CT47B1.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 CT47B1.stick_fig.jpg
Done
2020-06-19 01:59:42 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3905
Processing input file /cromwell_root/CT47B1.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 CT47B1.stick_fig.pdf
Done
2020-06-19 01:59:42 PM::INFO  Working with gene: BCORL1
2020-06-19 01:59:50 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3921
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 01:59:56 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3937
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 01:59:56 PM::INFO  Working with gene: CHD4
2020-06-19 02:00:02 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3953
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 02:00:09 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3969
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 02:00:09 PM::INFO  Working with gene: BGN
2020-06-19 02:00:15 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.3985
Processing input file /cromwell_root/BGN.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 BGN.stick_fig.jpg
Done
2020-06-19 02:00:22 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4001
Processing input file /cromwell_root/BGN.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 BGN.stick_fig.pdf
Done
2020-06-19 02:00:22 PM::INFO  Working with gene: SHCBP1L
2020-06-19 02:00:28 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4017
Processing input file /cromwell_root/SHCBP1L.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 SHCBP1L.stick_fig.jpg
Done
2020-06-19 02:00:35 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4033
Processing input file /cromwell_root/SHCBP1L.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 SHCBP1L.stick_fig.pdf
Done
2020-06-19 02:00:35 PM::INFO  Working with gene: NCKAP1
2020-06-19 02:00:42 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4049
Processing input file /cromwell_root/NCKAP1.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 NCKAP1.stick_fig.jpg
Done
2020-06-19 02:00:48 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4065
Processing input file /cromwell_root/NCKAP1.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 NCKAP1.stick_fig.pdf
Done
2020-06-19 02:00:48 PM::INFO  Working with gene: KLHL6
2020-06-19 02:00:56 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4081
Processing input file /cromwell_root/KLHL6.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 KLHL6.stick_fig.jpg
Done
2020-06-19 02:01:02 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4097
Processing input file /cromwell_root/KLHL6.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 KLHL6.stick_fig.pdf
Done
2020-06-19 02:01:02 PM::INFO  Working with gene: MAP2
2020-06-19 02:01:08 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4113
Processing input file /cromwell_root/MAP2.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 KNDC1. {ECO:0000250|UniProtKB:P20'} 
{> In mutfig at 516} 
Generating output file MAP2.stick_fig.jpg
Done
2020-06-19 02:01:15 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4129
Processing input file /cromwell_root/MAP2.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 KNDC1. {ECO:0000250|UniProtKB:P20'} 
{> In mutfig at 516} 
Generating output file MAP2.stick_fig.pdf
Done
2020-06-19 02:01:15 PM::INFO  Working with gene: BTK
2020-06-19 02:01:21 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4145
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 02:01:29 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4161
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 02:01:29 PM::INFO  Working with gene: METTL21C
2020-06-19 02:01:35 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4177
Processing input file /cromwell_root/METTL21C.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:
'S-adenosyl-L-methionine binding. {ECO:0000269|Ref.'} 
{> In mutfig at 516} 
Generating output file METTL21C.stick_fig.jpg
Done
2020-06-19 02:01:43 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4193
Processing input file /cromwell_root/METTL21C.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:
'S-adenosyl-L-methionine binding. {ECO:0000269|Ref.'} 
{> In mutfig at 516} 
Generating output file METTL21C.stick_fig.pdf
Done
2020-06-19 02:01:43 PM::INFO  Working with gene: PRKDC
2020-06-19 02:01:50 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4209
Processing input file /cromwell_root/PRKDC.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 PRKDC.stick_fig.jpg
Done
2020-06-19 02:01:56 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4225
Processing input file /cromwell_root/PRKDC.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 PRKDC.stick_fig.pdf
Done
2020-06-19 02:01:56 PM::INFO  Working with gene: SERPING1
2020-06-19 02:02:02 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4241
Processing input file /cromwell_root/SERPING1.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:
'Plasma protease C1 inhibitor. {ECO:0000269|PubMed:'} 
{> In mutfig at 516} 
Generating output file SERPING1.stick_fig.jpg
Done
2020-06-19 02:02:08 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4257
Processing input file /cromwell_root/SERPING1.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:
'Plasma protease C1 inhibitor. {ECO:0000269|PubMed:'} 
{> In mutfig at 516} 
Generating output file SERPING1.stick_fig.pdf
Done
2020-06-19 02:02:08 PM::INFO  Working with gene: SAFB2
2020-06-19 02:02:15 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4273
Processing input file /cromwell_root/SAFB2.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 SAFB2.stick_fig.jpg
Done
2020-06-19 02:02:21 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4289
Processing input file /cromwell_root/SAFB2.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 SAFB2.stick_fig.pdf
Done
2020-06-19 02:02:21 PM::INFO  Working with gene: ZNF786
2020-06-19 02:02:27 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4305
Processing input file /cromwell_root/ZNF786.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 ZNF786.stick_fig.jpg
Done
2020-06-19 02:02:33 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4321
Processing input file /cromwell_root/ZNF786.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 ZNF786.stick_fig.pdf
Done
2020-06-19 02:02:33 PM::INFO  Working with gene: COL6A5
2020-06-19 02:02:41 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4337
Processing input file /cromwell_root/COL6A5.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 COL6A5.stick_fig.jpg
Done
2020-06-19 02:02:47 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4353
Processing input file /cromwell_root/COL6A5.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 COL6A5.stick_fig.pdf
Done
2020-06-19 02:02:47 PM::INFO  Working with gene: FAM50A
2020-06-19 02:02:53 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4369
Processing input file /cromwell_root/FAM50A.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 FAM50A.stick_fig.jpg
Done
2020-06-19 02:02:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4385
Processing input file /cromwell_root/FAM50A.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 FAM50A.stick_fig.pdf
Done
2020-06-19 02:02:59 PM::INFO  Working with gene: CBX4
2020-06-19 02:03:06 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4401
Processing input file /cromwell_root/CBX4.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:
'Involved in interaction with HIST2H3A and RNF2. {E'} 
{> In mutfig at 516} 
Generating output file CBX4.stick_fig.jpg
Done
2020-06-19 02:03:12 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4417
Processing input file /cromwell_root/CBX4.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:
'Involved in interaction with HIST2H3A and RNF2. {E'} 
{> In mutfig at 516} 
Generating output file CBX4.stick_fig.pdf
Done
2020-06-19 02:03:12 PM::INFO  Working with gene: R3HCC1L
2020-06-19 02:03:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4433
Processing input file /cromwell_root/R3HCC1L.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 R3HCC1L.stick_fig.jpg
Done
2020-06-19 02:03:24 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4449
Processing input file /cromwell_root/R3HCC1L.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 R3HCC1L.stick_fig.pdf
Done
2020-06-19 02:03:24 PM::INFO  Working with gene: PDGFRA
2020-06-19 02:03:31 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4465
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 02:03:37 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4481
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 02:03:37 PM::INFO  Working with gene: TNK2
2020-06-19 02:03:46 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4497
Processing input file /cromwell_root/TNK2.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 SRC. {ECO:0000269|Pu'} 
{> In mutfig at 516} 
Generating output file TNK2.stick_fig.jpg
Done
2020-06-19 02:03:52 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4513
Processing input file /cromwell_root/TNK2.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 SRC. {ECO:0000269|Pu'} 
{> In mutfig at 516} 
Generating output file TNK2.stick_fig.pdf
Done
2020-06-19 02:03:52 PM::INFO  Working with gene: DISC1
2020-06-19 02:03:58 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4529
Processing input file /cromwell_root/DISC1.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 MAP1A. {ECO:0000269|PubMed:128129'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with TRAF3IP1. {ECO:0000269|PubMed:128'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with ATF4 and ATF5. {ECO:0000269|PubMe'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with PAFAH1B1. {ECO:0000269|PubMed:149'} 
{> In mutfig at 516} 
Generating output file DISC1.stick_fig.jpg
Done
2020-06-19 02:04:06 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4545
Processing input file /cromwell_root/DISC1.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 MAP1A. {ECO:0000269|PubMed:128129'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with TRAF3IP1. {ECO:0000269|PubMed:128'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with ATF4 and ATF5. {ECO:0000269|PubMe'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with PAFAH1B1. {ECO:0000269|PubMed:149'} 
{> In mutfig at 516} 
Generating output file DISC1.stick_fig.pdf
Done
2020-06-19 02:04:06 PM::INFO  Working with gene: SASS6
2020-06-19 02:04:12 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4561
Processing input file /cromwell_root/SASS6.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 SASS6.stick_fig.jpg
Done
2020-06-19 02:04:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4577
Processing input file /cromwell_root/SASS6.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 SASS6.stick_fig.pdf
Done
2020-06-19 02:04:18 PM::INFO  Working with gene: BNC1
2020-06-19 02:04:24 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4593
Processing input file /cromwell_root/BNC1.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:9'} 
{> In mutfig at 516} 
Generating output file BNC1.stick_fig.jpg
Done
2020-06-19 02:04:31 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4609
Processing input file /cromwell_root/BNC1.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:9'} 
{> In mutfig at 516} 
Generating output file BNC1.stick_fig.pdf
Done
2020-06-19 02:04:31 PM::INFO  Working with gene: TMCC1
2020-06-19 02:04:38 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4625
Processing input file /cromwell_root/TMCC1.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 TMCC1.stick_fig.jpg
Done
2020-06-19 02:04:46 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4641
Processing input file /cromwell_root/TMCC1.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 TMCC1.stick_fig.pdf
Done
2020-06-19 02:04:46 PM::INFO  Working with gene: CCDC122
2020-06-19 02:04:52 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4657
Processing input file /cromwell_root/CCDC122.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 CCDC122.stick_fig.jpg
Done
2020-06-19 02:04:58 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4673
Processing input file /cromwell_root/CCDC122.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 CCDC122.stick_fig.pdf
Done
2020-06-19 02:04:58 PM::INFO  Working with gene: ST3GAL5
2020-06-19 02:05:04 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4689
Processing input file /cromwell_root/ST3GAL5.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 ST3GAL5.stick_fig.jpg
Done
2020-06-19 02:05:12 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4705
Processing input file /cromwell_root/ST3GAL5.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 ST3GAL5.stick_fig.pdf
Done
2020-06-19 02:05:12 PM::INFO  Working with gene: FZR1
2020-06-19 02:05:18 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4721
Processing input file /cromwell_root/FZR1.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 FZR1.stick_fig.jpg
Done
2020-06-19 02:05:24 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4737
Processing input file /cromwell_root/FZR1.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 FZR1.stick_fig.pdf
Done
2020-06-19 02:05:24 PM::INFO  Working with gene: DMD
2020-06-19 02:05:31 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4753
Processing input file /cromwell_root/DMD.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 DMD.stick_fig.jpg
Done
2020-06-19 02:05:37 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4769
Processing input file /cromwell_root/DMD.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 DMD.stick_fig.pdf
Done
2020-06-19 02:05:37 PM::INFO  Working with gene: GTF2F1
2020-06-19 02:05:44 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4785
Processing input file /cromwell_root/GTF2F1.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 GTF2F1.stick_fig.jpg
Done
2020-06-19 02:05:52 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4801
Processing input file /cromwell_root/GTF2F1.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 GTF2F1.stick_fig.pdf
Done
2020-06-19 02:05:52 PM::INFO  Working with gene: NUP210L
2020-06-19 02:05:59 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4817
Processing input file /cromwell_root/NUP210L.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 NUP210L.stick_fig.jpg
Done
2020-06-19 02:06:05 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4833
Processing input file /cromwell_root/NUP210L.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 NUP210L.stick_fig.pdf
Done
2020-06-19 02:06:05 PM::INFO  Working with gene: ATF7IP
2020-06-19 02:06:11 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4849
Processing input file /cromwell_root/ATF7IP.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 SUMO. {ECO:0000269|PubMed:1675747'} 
{> In mutfig at 516} 
Generating output file ATF7IP.stick_fig.jpg
Done
2020-06-19 02:06:17 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4865
Processing input file /cromwell_root/ATF7IP.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 SUMO. {ECO:0000269|PubMed:1675747'} 
{> In mutfig at 516} 
Generating output file ATF7IP.stick_fig.pdf
Done
2020-06-19 02:06:17 PM::INFO  Working with gene: CYP11B1
2020-06-19 02:06:24 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4881
Processing input file /cromwell_root/CYP11B1.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 CYP11B1.stick_fig.jpg
Done
2020-06-19 02:06:30 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4897
Processing input file /cromwell_root/CYP11B1.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 CYP11B1.stick_fig.pdf
Done
2020-06-19 02:06:30 PM::INFO  Working with gene: POPDC3
2020-06-19 02:06:36 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4913
Processing input file /cromwell_root/POPDC3.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 POPDC3.stick_fig.jpg
Done
2020-06-19 02:06:42 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4929
Processing input file /cromwell_root/POPDC3.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 POPDC3.stick_fig.pdf
Done
2020-06-19 02:06:42 PM::INFO  Working with gene: MAP7D1
2020-06-19 02:06:50 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4945
Processing input file /cromwell_root/MAP7D1.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 MAP7D1.stick_fig.jpg
Done
2020-06-19 02:06:56 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4961
Processing input file /cromwell_root/MAP7D1.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 MAP7D1.stick_fig.pdf
Done
2020-06-19 02:06:56 PM::INFO  Working with gene: SERPINB2
2020-06-19 02:07:02 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4977
Processing input file /cromwell_root/SERPINB2.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 SERPINB2.stick_fig.jpg
Done
2020-06-19 02:07:08 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.4993
Processing input file /cromwell_root/SERPINB2.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 SERPINB2.stick_fig.pdf
Done
2020-06-19 02:07:08 PM::INFO  Working with gene: EIF2S3L
2020-06-19 02:07:15 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5009
Processing input file /cromwell_root/EIF2S3L.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 EIF2S3L.stick_fig.jpg
Done
2020-06-19 02:07:22 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5025
Processing input file /cromwell_root/EIF2S3L.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 EIF2S3L.stick_fig.pdf
Done
2020-06-19 02:07:22 PM::INFO  Working with gene: GTF3C1
2020-06-19 02:07:28 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5041
Processing input file /cromwell_root/GTF3C1.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 GTF3C1.stick_fig.jpg
Done
2020-06-19 02:07:34 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5057
Processing input file /cromwell_root/GTF3C1.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 GTF3C1.stick_fig.pdf
Done
2020-06-19 02:07:34 PM::INFO  Working with gene: CLP1
2020-06-19 02:07:41 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5073
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 02:07:48 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5089
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 02:07:48 PM::INFO  Working with gene: RREB1
2020-06-19 02:07:56 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5105
Processing input file /cromwell_root/RREB1.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 RREB1.stick_fig.jpg
Done
2020-06-19 02:08:03 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5121
Processing input file /cromwell_root/RREB1.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 RREB1.stick_fig.pdf
Done
2020-06-19 02:08:03 PM::INFO  Working with gene: MMP8
2020-06-19 02:08:09 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5137
Processing input file /cromwell_root/MMP8.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 MMP8.stick_fig.jpg
Done
2020-06-19 02:08:15 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5153
Processing input file /cromwell_root/MMP8.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 MMP8.stick_fig.pdf
Done
2020-06-19 02:08:15 PM::INFO  Working with gene: SLC35D3
2020-06-19 02:08:23 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5169
Processing input file /cromwell_root/SLC35D3.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 SLC35D3.stick_fig.jpg
Done
2020-06-19 02:08:29 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.5185
Processing input file /cromwell_root/SLC35D3.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 SLC35D3.stick_fig.pdf
Done
2020-06-19 02:08:29 PM::INFO  Runtime: 35.9531553825 minutes
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.a70cdde9/out.6
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.a70cdde9/err.6
  adding: SERPING1.stick_fig.jpg (deflated 32%)
  adding: RNF43.stick_fig.txt (deflated 74%)
  adding: FBXW7.stick_fig.txt (deflated 79%)
  adding: SAMD7.stick_fig.pdf (deflated 30%)
  adding: EGFR.stick_fig.txt (deflated 87%)
  adding: SHCBP1L.stick_fig.txt (deflated 65%)
  adding: DENND2A.stick_fig.pdf (deflated 30%)
  adding: CUL4B.stick_fig.jpg (deflated 27%)
  adding: CR2.stick_fig.txt (deflated 70%)
  adding: GPR174.stick_fig.pdf (deflated 30%)
  adding: PZP.stick_fig.txt (deflated 73%)
  adding: PUS1.stick_fig.txt (deflated 68%)
  adding: DFNA5.stick_fig.pdf (deflated 30%)
  adding: SEC31A.stick_fig.txt (deflated 69%)
  adding: ESRP1.stick_fig.jpg (deflated 29%)
  adding: MEDAG.stick_fig.txt (deflated 60%)
  adding: CTNNB1.stick_fig.pdf (deflated 22%)
  adding: CYBB.stick_fig.jpg (deflated 25%)
  adding: RNF2.stick_fig.txt (deflated 64%)
  adding: CLP1.stick_fig.pdf (deflated 35%)
  adding: LMAN1.stick_fig.pdf (deflated 32%)
  adding: ZNF853.stick_fig.jpg (deflated 33%)
  adding: FYB.stick_fig.jpg (deflated 20%)
  adding: CLP1.stick_fig.txt (deflated 59%)
  adding: FYB.stick_fig.txt (deflated 69%)
  adding: TP53TG5.stick_fig.txt (deflated 62%)
  adding: CPZ.stick_fig.jpg (deflated 27%)
  adding: ADGRE1.stick_fig.jpg (deflated 28%)
  adding: JAK1.stick_fig.pdf (deflated 29%)
  adding: RASA1.stick_fig.pdf (deflated 27%)
  adding: NFE2L2.stick_fig.txt (deflated 75%)
  adding: RPL22.stick_fig.jpg (deflated 40%)
  adding: GLRA4.stick_fig.txt (deflated 66%)
  adding: PIGO.stick_fig.txt (deflated 63%)
  adding: FAM50A.stick_fig.jpg (deflated 32%)
  adding: LMAN1.stick_fig.jpg (deflated 26%)
  adding: KRIT1.stick_fig.jpg (deflated 27%)
  adding: PZP.stick_fig.pdf (deflated 25%)
  adding: FZR1.stick_fig.jpg (deflated 37%)
  adding: FAM50A.stick_fig.pdf (deflated 30%)
  adding: BTK.stick_fig.pdf (deflated 28%)
  adding: GRIK3.stick_fig.pdf (deflated 24%)
  adding: XPO5.stick_fig.pdf (deflated 30%)
  adding: PRKDC.stick_fig.pdf (deflated 22%)
  adding: KRTAP10-4.stick_fig.jpg (deflated 29%)
  adding: KMT2D.stick_fig.jpg (deflated 11%)
  adding: TMEM39A.stick_fig.jpg (deflated 34%)
  adding: BNC2.stick_fig.jpg (deflated 28%)
  adding: NCKAP1.stick_fig.jpg (deflated 36%)
  adding: R3HCC1L.stick_fig.jpg (deflated 42%)
  adding: EGFL6.stick_fig.txt (deflated 67%)
  adding: ARHGAP35.stick_fig.txt (deflated 72%)
  adding: TIGIT.stick_fig.txt (deflated 65%)
  adding: IFNAR1.stick_fig.jpg (deflated 32%)
  adding: CCDC122.stick_fig.txt (deflated 60%)
  adding: TSNAX.stick_fig.pdf (deflated 36%)
  adding: TLR7.stick_fig.txt (deflated 74%)
  adding: BCORL1.stick_fig.txt (deflated 73%)
  adding: TMCC1.stick_fig.jpg (deflated 40%)
  adding: EIF1AX.stick_fig.pdf (deflated 36%)
  adding: GLI1.stick_fig.jpg (deflated 18%)
  adding: LMNB2.stick_fig.pdf (deflated 30%)
  adding: BSX.stick_fig.pdf (deflated 36%)
  adding: MS4A14.stick_fig.pdf (deflated 25%)
  adding: SAMD9.stick_fig.pdf (deflated 25%)
  adding: PPM1D.stick_fig.jpg (deflated 30%)
  adding: MGA.stick_fig.jpg (deflated 16%)
  adding: GTF3C1.stick_fig.txt (deflated 77%)
  adding: ZNF300.stick_fig.jpg (deflated 32%)
  adding: AL358113.1.stick_fig.txt (deflated 56%)
  adding: SAMD9.stick_fig.txt (deflated 78%)
  adding: H2AFY2.stick_fig.pdf (deflated 40%)
  adding: CD300LG.stick_fig.pdf (deflated 33%)
  adding: TFDP1.stick_fig.pdf (deflated 30%)
  adding: IFNAR1.stick_fig.txt (deflated 59%)
  adding: XPO5.stick_fig.txt (deflated 64%)
  adding: DISC1.stick_fig.jpg (deflated 15%)
  adding: ARHGAP35.stick_fig.jpg (deflated 18%)
  adding: BNC2.stick_fig.txt (deflated 73%)
  adding: MAP7D1.stick_fig.txt (deflated 60%)
  adding: DMD.stick_fig.jpg (deflated 16%)
  adding: CT47B1.stick_fig.pdf (deflated 32%)
  adding: SCAF4.stick_fig.pdf (deflated 27%)
  adding: PCDHGA1.stick_fig.jpg (deflated 25%)
  adding: CTCF.stick_fig.pdf (deflated 23%)
  adding: CUL4B.stick_fig.pdf (deflated 30%)
  adding: RBM27.stick_fig.jpg (deflated 35%)
  adding: GLRA4.stick_fig.pdf (deflated 31%)
  adding: RNF43.stick_fig.jpg (deflated 30%)
  adding: CDKN2A.stick_fig.jpg (deflated 22%)
  adding: ATF7IP.stick_fig.txt (deflated 69%)
  adding: COL6A5.stick_fig.pdf (deflated 26%)
  adding: USP13.stick_fig.pdf (deflated 29%)
  adding: CUL3.stick_fig.pdf (deflated 27%)
  adding: ARHGAP35.stick_fig.pdf (deflated 24%)
  adding: MGA.stick_fig.pdf (deflated 22%)
  adding: TP53TG5.stick_fig.jpg (deflated 38%)
  adding: ZNF800.stick_fig.pdf (deflated 31%)
  adding: BNC1.stick_fig.jpg (deflated 22%)
  adding: AFM.stick_fig.txt (deflated 71%)
  adding: CYP11B1.stick_fig.pdf (deflated 26%)
  adding: TNK2.stick_fig.jpg (deflated 19%)
  adding: BSX.stick_fig.jpg (deflated 38%)
  adding: UCHL5.stick_fig.txt (deflated 62%)
  adding: TMEM202.stick_fig.pdf (deflated 37%)
  adding: CYP11B1.stick_fig.txt (deflated 70%)
  adding: ESRP1.stick_fig.txt (deflated 75%)
  adding: METTL21C.stick_fig.jpg (deflated 34%)
  adding: EGFL6.stick_fig.pdf (deflated 29%)
  adding: TMCC1.stick_fig.pdf (deflated 33%)
  adding: IPO7.stick_fig.txt (deflated 63%)
  adding: PDGFRA.stick_fig.txt (deflated 74%)
  adding: stdout