I have been testing the germline CNV workflow. I downloaded WDLs from Github and installed new docker image of GATK (latest on Friday).
I have prepared project folder:
-- bams_cnv / 60 BAMs and BAIs (symlink)
-- germline_CNV / inputs.json cnv_germline_cohort_workflow.wdl ploidy_table.csv wes_intervals.bed
-- hg19 / hg19 reference stored here
I am running this command:
java -jar cromwell-50.jar run cnv_germline_cohort_workflow.wdl --inputs ./germline_CNV/inputs.json
The workflow runs with some warning (for like 1 hour) but then it was hanging on "WaitingForReturnCode" for two days and then it gets SIGKILL and its aborted.
Could you please navigate me, where is the mistake?
I am uploading workflow log and inputs.json file.
I am running workflow locally on Ubuntu 18, 64 GB Ram and 16 core CPU.
Please sign in to leave a comment.