Thanks for this software -- I am having an issue processing a run through iGUIDE where the pipeline fails at the iGUIDE_evaluation at nearly 99% completion. I can't seem to figure out why exactly this errors out. I am processing with a 128Gb memory instance.
My colleague has successfully processed this exact data but with the R2leadMismatch : 15 specified in the config.yml whereas I have this set to R2leadMismatch : 3. I am calling the pipeline via iguide run IP095/configs/IP095.yml -- --notemp --nolock --cores 14 --restart-times 5.
Here's the last few lines of the snakelike log:
[Fri Jan 22 21:48:53 2021]
rule iguide_evaluation:
input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
jobid: 86
resources: mem_mb=8000
Trying to restart job 86.
[Fri Jan 22 21:49:02 2021]
rule iguide_evaluation:
input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
jobid: 86
resources: mem_mb=16000
Trying to restart job 86.
[Fri Jan 22 21:49:10 2021]
rule iguide_evaluation:
input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
jobid: 86
resources: mem_mb=24000
Trying to restart job 86.
[Fri Jan 22 21:49:19 2021]
rule iguide_evaluation:
input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
jobid: 86
resources: mem_mb=32000
Trying to restart job 86.
[Fri Jan 22 21:49:28 2021]
rule iguide_evaluation:
input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
jobid: 86
resources: mem_mb=40000
Trying to restart job 86.
[Fri Jan 22 21:49:37 2021]
rule iguide_evaluation:
input: /home/ubuntu/iGUIDE/analysis/IP095/output/incorp_sites.IP095.rds
output: /home/ubuntu/iGUIDE/analysis/IP095/output/iguide.eval.IP095.rds, /home/ubuntu/iGUIDE/analysis/IP095/output/IP095.eval.stat
log: /home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
jobid: 86
resources: mem_mb=48000
[Fri Jan 22 21:55:14 2021]
Finished job 659.
894 of 907 steps (99%) done
[Fri Jan 22 22:02:39 2021]
Finished job 658.
895 of 907 steps (99%) done
[Fri Jan 22 22:05:52 2021]
Finished job 661.
896 of 907 steps (99%) done
[Fri Jan 22 22:08:18 2021]
Finished job 660.
897 of 907 steps (99%) done
[Fri Jan 22 22:10:58 2021]
Finished job 662.
898 of 907 steps (99%) done
[Fri Jan 22 22:18:54 2021]
Finished job 664.
899 of 907 steps (99%) done
[Fri Jan 22 22:41:27 2021]
Finished job 663.
900 of 907 steps (99%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/ubuntu/iGUIDE/.snakemake/log/2021-01-22T183409.805924.snakemake.log
Hi Chris,
Thanks for this software -- I am having an issue processing a run through iGUIDE where the pipeline fails at the
iGUIDE_evaluation
at nearly 99% completion. I can't seem to figure out why exactly this errors out. I am processing with a 128Gb memory instance.My colleague has successfully processed this exact data but with the
R2leadMismatch : 15
specified in the config.yml whereas I have this set toR2leadMismatch : 3
. I am calling the pipeline viaiguide run IP095/configs/IP095.yml -- --notemp --nolock --cores 14 --restart-times 5
.Here's the last few lines of the snakelike log:
/home/ubuntu/iGUIDE/analysis/IP095/logs/IP095.eval.log
:Any help would be much appreciated. Thanks.