Open tgebo opened 3 months ago
job is still currently running 158093
This seems to be related a bug with the directory being created by Spark and then having issues with removing it; the fix is likely with updating the GATK version used in align-DNA for Spark to include bugfixes since the version we currently use. In the meantime, a workaround can be to use Picard markduplicates instead of Spark at the cost of runtime
okay, I just relaunched it changing the Spark setting under alignDNA. Thanks for looking into it.
@yashpatel6 I got another error after changing the Spark setting^.
/hot/user/tgebo/Brohl-Gonzalez-SARC-ERSM_metapipeline/WGS/workdir/6b/d2dd9f269098c398387f51a7aacb36/.command.log
Looks like it just got Killed during MarkDuplicates. Please help.
Describe the issue A clear and concise description of what the issue is. Please include the following in your issue report along with any explicit errors observed
5.3.1
Slurmdev
F72
/hot/user/alfgonzalez/project/project-LAND-SARC/project-SARC-LAND/pipeline/16.Brohl-Gonzalez-SARC-ERSM/metapipeline-DNA/config/WGS_BGSAERSM_metapipeline-DNA.config
/hot/user/tgebo/Brohl-Gonzalez-SARC-ERSM_metapipeline/WGS/workdir
/hot/user/tgebo/Brohl-Gonzalez-SARC-ERSM_metapipeline/WGS/workdir/86/b5d3d08dff9f2054d10c08c67778ab/.command.log
Both the working_dir and output_dir are my user directory. I've tried submitting using both the python submission script (command above) as well as this script
/hot/user/alfgonzalez/project/project-LAND-SARC/project-SARC-LAND/pipeline/16.Brohl-Gonzalez-SARC-ERSM/metapipeline-DNA/run_script/WGS_launch_metapipeline-DNA-5.3.1_BGSAERSM.sh
and see the same error time after time.