2019-10-22 02:04:03 AM::INFO  Working with gene: TP53
2019-10-22 02:04:14 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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
2019-10-22 02:04:22 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.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
2019-10-22 02:04:22 AM::INFO  Working with gene: EGFR
2019-10-22 02:04:28 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.49
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
2019-10-22 02:04:35 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.65
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
2019-10-22 02:04:35 AM::INFO  Working with gene: KRAS
2019-10-22 02:04:43 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.81
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
2019-10-22 02:04:50 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.97
Processing input file /cromwell_root/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
2019-10-22 02:04:50 AM::INFO  Working with gene: STK11
2019-10-22 02:04:59 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.113
Processing input file /cromwell_root/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
2019-10-22 02:05:05 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.129
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
2019-10-22 02:05:05 AM::INFO  Working with gene: KEAP1
2019-10-22 02:05:13 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.145
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
2019-10-22 02:05:20 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.161
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
2019-10-22 02:05:20 AM::INFO  Working with gene: RB1
2019-10-22 02:05:27 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.177
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
2019-10-22 02:05:34 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.193
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
2019-10-22 02:05:34 AM::INFO  Working with gene: IL21R
2019-10-22 02:05:42 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.209
Processing input file /cromwell_root/IL21R.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file IL21R.stick_fig.jpg
Done
2019-10-22 02:05:48 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.225
Processing input file /cromwell_root/IL21R.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file IL21R.stick_fig.pdf
Done
2019-10-22 02:05:48 AM::INFO  Working with gene: BIRC6
2019-10-22 02:05:55 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.241
Processing input file /cromwell_root/BIRC6.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file BIRC6.stick_fig.jpg
Done
2019-10-22 02:06:02 AM::INFO  mutfig output: Warning: No display specified.  You will not be able to display graphics on the screen.
Opening log file:  /root/java.log.257
Processing input file /cromwell_root/BIRC6.stick_fig.txt
Please ignore the following warning message:
{Warning: Trust-region-reflective algorithm does not solve this type of problem,
using active-set algorithm. You could also try the interior-point-convex
algorithm: set the Algorithm option to interior-point-convex and rerun. For
more help, see Choosing the Algorithm in the documentation.} 
{> In quadprog at 371
  In find_text_pos at 42
  In mutfig at 342} 
Generating output file BIRC6.stick_fig.pdf
Done
2019-10-22 02:06:02 AM::INFO  Runtime: 2.03723391692 minutes
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.8cff0637/err.6
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.8cff0637/out.6
  adding: STK11.stick_fig.pdf (deflated 26%)
  adding: TP53.stick_fig.txt (deflated 79%)
  adding: gcs_transfer.sh (deflated 75%)
  adding: KRAS.stick_fig.pdf (deflated 25%)
  adding: BIRC6.stick_fig.jpg (deflated 32%)
  adding: KRAS.stick_fig.jpg (deflated 29%)
  adding: BIRC6.stick_fig.txt (deflated 57%)
  adding: KEAP1.stick_fig.pdf (deflated 29%)
  adding: script (deflated 75%)
  adding: stdout