Open nandankita opened 3 years ago
First of all I think cromwell-42.jar
is outdated. Please try with cromwell-52.jar instead.
caper run ... --cromwell https://github.com/broadinstitute/cromwell/releases/download/52/cromwell-52.jar
Can you check any logs from the main job (where caper run ...
runs on)?
How big is your sample? What is the size of FASTQs or BAMs?
I am running pipeline version: v1.9.2. My pipeline runs till atac.macs2_signal_track, then the next atac.qc_report is not triggered. I have following questions about the pipeline:
Currently I am running the pipeline with following command:
sbatch -p all -J atac_submit --export=ALL --mem 3G -t 5-0 --wrap "caper run /pipelines/encode-atac-seq-pipeline-v1.9.2/atac.wdl -c /pipelines/encode-atac-seq-pipeline-v1.9.2/caper.conf --cromwell /pipelines/encode-atac-seq-pipeline-v1.9.2/cromwell-42.jar --womtool /pipelines/encode-atac-seq-pipeline-v1.9.2/womtool-52.jar -i input.json --singularity /pipelines/encode-atac-seq-pipeline-v1.9.2/singularity/atac-seq-pipeline_v1.9.2.sif"
In my caper.conf I have following lines uncommented:
Any help would be appreciated. Please let me know if you need any more detail for this question.