Open ambeys opened 3 years ago
Check if SGE Parallel Environment openmp
exists.
$ qconf -sp
Post caper run
's STDOUT.
caper troubleshoot
is for server mode only.
Also ignore unsupported
warnings in cromwell.out
.
$ qconf -sp
yes, openmp is there as PE.
These were the last lines of the caper run. the stdout it says it doesn't exist. 2020-11-18 14:51:19,399|caper.cromwell|INFO| Workflow failed. Auto-troubleshooting...
==== NAME=chip.read_genome_tsv, STATUS=Failed, PARENT= SHARD_IDX=-1, RC=-1, JOB_ID=15841 START=2020-11-18T20:50:59.365Z, END=2020-11-18T20:51:03.723Z STDOUT=/home/ambey/mnt/Genoma/amedina/ambey/CAPER/caper_out/chip/2668d99e-f85e-4481-986e-52eb1f5e880a/call-read_genome_tsv/execution/stdout STDERR=/home/ambey/mnt/Genoma/amedina/ambey/CAPER/caper_out/chip/2668d99e-f85e-4481-986e-52eb1f5e880a/call-read_genome_tsv/execution/stderr 2020-11-18 14:51:19,400|caper.nb_subproc_thread|ERROR| Subprocess failed. returncode=1 2020-11-18 14:51:19,400|caper.cli|ERROR| Check stdout/stderr in /mnt/Genoma/amedina/ambey/chip-seq-pipeline2/ExampleRun/cromwell.out
Describe the bug
I am trying to run caper for chip-seq pipeline for Transcription factor. The dry run shows that caper run is fine. But when trying with the example file or my own input.json file it is giving me error failed to connect Cromwell server and in crowwell.out it shows unsupported backend. SGE mode starts a job properly, then fails, I guess there is certain issue with configuration with the age for Cromwell. May be we have to add some options in order to work correctly in our cluster. I tried it in mac and My colleague did try on window platform as well. and report the same error. i went through all the documentation and tried to fix with different ways but somehow it is not running. It has been since 3 weeks that we are stuck in this.
OS/Platform
Caper configuration file
Paste contents of
/home/ambey/.caper/default.conf
.Input JSON file
Command used
Troubleshooting result
cromwell.out.txt