Pipeline Fails at Peak Calling

Describe the bug

I am attempting to run the pipeline with a custom genome. However, when running the pipeline the peak calling step fails. Ive attached the custom TSV, JSON, and error message below.

OS/Platform

OS/Platform: Ubuntu 18.04
Conda version: conda 23.1.0
Pipeline version: 2.2.2
Caper version: caper 2.2.3

Caper configuration file

backend=local

# Local directory for localized files and Cromwell's intermediate files.
# If not defined then Caper will make .caper_tmp/ on CWD or `local-out-dir`.
# /tmp is not recommended since Caper store localized data files here.
local-loc-dir=/home/arian/DomainAdaptation/chicken-liver-data/caper-results

cromwell=/home/arian/.caper/cromwell_jar/cromwell-82.jar
womtool=/home/arian/.caper/womtool_jar/womtool-82.jar

Input JSON file

{
    "atac.pipeline_type" : "dnase",
    "atac.genome_tsv" : "/home/arian/DomainAdaptation/chicken-liver-data/bGalGal1_Genome.tsv",
    "atac.fastqs_rep1_R1" : [
        "/home/arian/DomainAdaptation/chicken-liver-data/SRR12697256_1.fastq"
    ],
    "atac.fastqs_rep1_R2" : [
        "/home/arian/DomainAdaptation/chicken-liver-data/SRR12697256_2.fastq"
    ],
    "atac.fastqs_rep2_R1" : [
        "/home/arian/DomainAdaptation/chicken-liver-data/SRR12697257_1.fastq"
    ],
    "atac.fastqs_rep2_R2" : [
        "/home/arian/DomainAdaptation/chicken-liver-data/SRR12697257_2.fastq"
    ],
    "atac.multimapping" : 0,
    "atac.enable_xcor" : false,
    "atac.cap_num_peak" : 300000,
    "atac.filter_chrs" : ["chrM"],
    "atac.smooth_win" : 150,
    "atac.enable_idr" : true,
    "atac.idr_thresh" : 0.1,
    "atac.enable_preseq" : false,
    "atac.enable_jsd" : false,
    "atac.enable_tss_enrich" : false,
    "atac.enable_annot_enrich" : false,
    "atac.paired_end" : true
}

Troubleshooting result

If you ran caper run without Caper server then Caper automatically runs a troubleshooter for failed workflows. Find troubleshooting result in the bottom of Caper's screen log.

If you ran caper submit with a running Caper server then first find your workflow ID (1st column) with caper list and run caper debug [WORKFLOW_ID].

Paste troubleshooting result.

Found failures:
[
    {
        "causedBy": [
            {
                "causedBy": [],
                "message": "Job atac.call_peak:2:2 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
            },
            {
                "message": "Job atac.call_peak_pr2:2:2 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.",
                "causedBy": []
            },
            {
                "causedBy": [],
                "message": "Job atac.call_peak_pr1:2:2 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
            }
        ],
        "message": "Workflow failed"
    }
]

ENCODE-DCC / atac-seq-pipeline