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ENCODE-DCC / atac-seq-pipeline

ENCODE ATAC-seq pipeline
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question about qc_report and metadata.json #315

Open nandankita opened 3 years ago

nandankita commented 3 years ago

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:

  1. Is there a way to restart the pipeline from wherever it stopped? e.g. from atac.qc_report step?

  2. Where should I look for the exact reason of why atac.qc_report is not triggered? I looked into slurm.out, cromwell-workflow-logs/workflow.afa784a3-7030-4b68-99b2-9ba0f61812a2.log but nothing mentioned.

  3. What will be the command to generate metadata.json file manually? Since the pipeline is not finished, it is not generated automatically as I understand but I see all other output except call-qc_report are there. Hence I want to generate metadata.json and run croo.

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:

backend=slurm
show-completed-task=True
no-server-heartbeat=True

Any help would be appreciated. Please let me know if you need any more detail for this question.

leepc12 commented 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First of all I think cromwell-42.jar is outdated.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?