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ENCODE-DCC / atac-seq-pipeline

ENCODE ATAC-seq pipeline
MIT License
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Pipeline got stuck at task=atac.read_genome_tsv:-1 #364

Open thaorope opened 2 years ago

thaorope commented 2 years ago

Describe the bug

I tried to run this pipeline multiple times, and it kept getting stalled at task=atac.read_genome_tsv:-1. But there's no error message. It only stopped when timeout.

f1ce-42e9-8f41-86352133dd3d, task=atac.read_genome_tsv:-1, retry=0, status=WaitingForReturnCode slurmstepd: error: JOB 47286066 ON compute-e-16-198 CANCELLED AT 2022-01-16T09:26:18 DUE TO TIME LIMIT

OS/Platform

Caper configuration file

Paste contents of ~/.caper/default.conf.

slurm-partition=medium
slurm-account=knipe_dmk2
local-hash-strat=path+modtime
local-loc-dir=/home/tht900/ATAC-seq-testing/caper_temp
cromwell=/home/tht900/.caper/cromwell_jar/cromwell-65.jar
womtool=/home/tht900/.caper/womtool_jar/womtool-65.jar```

PASTE CAPER CONF CONTENTS HERE

Input JSON file

Paste contents of your input JSON file.

{
    "atac.pipeline_type" : "atac",
    "atac.genome_tsv" : "https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v3/hg38.tsv",
    "atac.fastqs_rep1_R1" : [
        "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz",
        "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz"
    ],
    "atac.fastqs_rep1_R2" : [
        "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz",
        "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz"
    ],
    "atac.fastqs_rep2_R1" : [
        "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz",
        "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz",
        "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz",
        "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz",
        "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz",
        "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz"
    ],
    "atac.fastqs_rep2_R2" : [
         "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz",
         "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz",
         "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz",
         "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz",
         "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz",
         "https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz"
    ],
    "atac.paired_end" : true,
    "atac.auto_detect_adapter" : true,
    "atac.enable_xcor" : true,
    "atac.title" : "ENCSR356KRQ (subsampled 1/400)",
    "atac.description" : "ATAC-seq on primary keratinocytes in day 0.0 of differentiation"
}
leepc12 commented 2 years ago

Please upload your cromwell.out*