2019-11-13 03:29:07 PM::INFO  Working with gene: PIK3CA
2019-11-13 03:29:23 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.16
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
2019-11-13 03:29:30 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.33
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
2019-11-13 03:29:30 PM::INFO  Working with gene: TP53
2019-11-13 03:29:38 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.49
Processing input file /cromwell_root/TP53.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
{Warning: incomplete command in TeX text string:
'Interaction with CCAR2. {ECO:0000269|PubMed:257328'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with HRMT1L2. {ECO:0000269|PubMed:1518'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Required for interaction with ZNF385A. {ECO:000026'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Required for interaction with FBXO42. {ECO:0000269'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with E4F1. {ECO:0000269|PubMed:1064499'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with CARM1. {ECO:0000269|PubMed:151867'} 
{> In mutfig at 516} 
Generating output file TP53.stick_fig.jpg
Done
2019-11-13 03:29:45 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.65
Processing input file /cromwell_root/TP53.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
{Warning: incomplete command in TeX text string:
'Interaction with CCAR2. {ECO:0000269|PubMed:257328'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with HRMT1L2. {ECO:0000269|PubMed:1518'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Required for interaction with ZNF385A. {ECO:000026'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Required for interaction with FBXO42. {ECO:0000269'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with E4F1. {ECO:0000269|PubMed:1064499'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with CARM1. {ECO:0000269|PubMed:151867'} 
{> In mutfig at 516} 
Generating output file TP53.stick_fig.pdf
Done
2019-11-13 03:29:45 PM::INFO  Working with gene: PTEN
2019-11-13 03:29:51 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.81
Processing input file /cromwell_root/PTEN.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
{Warning: incomplete command in TeX text string:
'Required for interaction with NOP53. {ECO:0000269|'} 
{> In mutfig at 516} 
Generating output file PTEN.stick_fig.jpg
Done
2019-11-13 03:29:58 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.97
Processing input file /cromwell_root/PTEN.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
{Warning: incomplete command in TeX text string:
'Required for interaction with NOP53. {ECO:0000269|'} 
{> In mutfig at 516} 
Generating output file PTEN.stick_fig.pdf
Done
2019-11-13 03:29:58 PM::INFO  Working with gene: CDH1
2019-11-13 03:30:04 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.113
Processing input file /cromwell_root/CDH1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file CDH1.stick_fig.jpg
Done
2019-11-13 03:30:10 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.129
Processing input file /cromwell_root/CDH1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file CDH1.stick_fig.pdf
Done
2019-11-13 03:30:10 PM::INFO  Working with gene: MAP3K1
2019-11-13 03:30:16 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.145
Processing input file /cromwell_root/MAP3K1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file MAP3K1.stick_fig.jpg
Done
2019-11-13 03:30:22 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.161
Processing input file /cromwell_root/MAP3K1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file MAP3K1.stick_fig.pdf
Done
2019-11-13 03:30:22 PM::INFO  Working with gene: AKT1
2019-11-13 03:30:29 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.177
Processing input file /cromwell_root/AKT1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file AKT1.stick_fig.jpg
Done
2019-11-13 03:30:35 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.193
Processing input file /cromwell_root/AKT1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file AKT1.stick_fig.pdf
Done
2019-11-13 03:30:35 PM::INFO  Working with gene: GATA3
2019-11-13 03:30:43 PM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.209
Processing input file /cromwell_root/GATA3.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file GATA3.stick_fig.jpg
Done
2019-11-13 03:30:49 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.225
Processing input file /cromwell_root/GATA3.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file GATA3.stick_fig.pdf
Done
2019-11-13 03:30:49 PM::INFO  Working with gene: CBFB
2019-11-13 03:30:55 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.241
Processing input file /cromwell_root/CBFB.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file CBFB.stick_fig.jpg
Done
2019-11-13 03:31:02 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.257
Processing input file /cromwell_root/CBFB.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file CBFB.stick_fig.pdf
Done
2019-11-13 03:31:02 PM::INFO  Working with gene: KMT2C
2019-11-13 03:31:08 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.273
Processing input file /cromwell_root/KMT2C.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file KMT2C.stick_fig.jpg
Done
2019-11-13 03:31:14 PM::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/KMT2C.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file KMT2C.stick_fig.pdf
Done
2019-11-13 03:31:14 PM::INFO  Working with gene: SF3B1
2019-11-13 03:31:20 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.305
Processing input file /cromwell_root/SF3B1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. 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 PPP1R8. {ECO:0000269|PubMed:12105'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with PHF5A. {ECO:0000269|PubMed:277206'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with SF3B3 and SF3B5. {ECO:0000269|Pub'} 
{> In mutfig at 516} 
Generating output file SF3B1.stick_fig.jpg
Done
2019-11-13 03:31:26 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.321
Processing input file /cromwell_root/SF3B1.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. 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 PPP1R8. {ECO:0000269|PubMed:12105'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with PHF5A. {ECO:0000269|PubMed:277206'} 
{> In mutfig at 516} 
{Warning: incomplete command in TeX text string:
'Interaction with SF3B3 and SF3B5. {ECO:0000269|Pub'} 
{> In mutfig at 516} 
Generating output file SF3B1.stick_fig.pdf
Done
2019-11-13 03:31:26 PM::INFO  Working with gene: ARID1A
2019-11-13 03:31:33 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.337
Processing input file /cromwell_root/ARID1A.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
{Warning: incomplete command in TeX text string:
'Nuclear localization signal. {ECO:0000269|PubMed:2'} 
{> In mutfig at 516} 
Generating output file ARID1A.stick_fig.jpg
Done
2019-11-13 03:31:39 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.353
Processing input file /cromwell_root/ARID1A.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
{Warning: incomplete command in TeX text string:
'Nuclear localization signal. {ECO:0000269|PubMed:2'} 
{> In mutfig at 516} 
Generating output file ARID1A.stick_fig.pdf
Done
2019-11-13 03:31:39 PM::INFO  Working with gene: MLLT4
2019-11-13 03:31:46 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.369
Processing input file /cromwell_root/MLLT4.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file MLLT4.stick_fig.jpg
Done
2019-11-13 03:31:52 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.385
Processing input file /cromwell_root/MLLT4.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file MLLT4.stick_fig.pdf
Done
2019-11-13 03:31:52 PM::INFO  Runtime: 2.86548870007 minutes
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.6543cd07/out.6
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.6543cd07/err.6
  adding: KMT2C.stick_fig.txt (deflated 64%)
  adding: stderr (stored 0%)
  adding: gcs_delocalization.sh (deflated 85%)
  adding: SF3B1.stick_fig.jpg (deflated 26%)
  adding: CBFB.stick_fig.txt (deflated 30%)
  adding: CDH1.stick_fig.txt (deflated 65%)
  adding: CBFB.stick_fig.pdf (deflated 40%)
  adding: GATA3.stick_fig.txt (deflated 60%)
  adding: ARID1A.stick_fig.txt (deflated 65%)
  adding: CBFB.stick_fig.jpg (deflated 55%)
  adding: GATA3.stick_fig.jpg (deflated 32%)
  adding: MAP3K1.stick_fig.pdf (deflated 27%)
  adding: KMT2C.stick_fig.jpg (deflated 24%)
  adding: PIK3CA.stick_fig.jpg (deflated 42%)
  adding: MAP3K1.stick_fig.txt (deflated 66%)
  adding: PTEN.stick_fig.pdf (deflated 33%)
  adding: SF3B1.stick_fig.pdf (deflated 35%)
  adding: SF3B1.stick_fig.txt (deflated 67%)
  adding: AKT1.stick_fig.txt (deflated 65%)
  adding: MAP3K1.stick_fig.jpg (deflated 20%)
  adding: stdout