failed with test data

[brainfo]

OS/Platform

• OS/Platform: Ubuntu 20.04.3 LTS
• Conda version: conda 4.11.0
• Pipeline version: v1.1.8
• Caper version: v2.1.3

Caper configuration file

backend=local

# Hashing strategy for call-caching (3 choices)
# This parameter is for local (local/slurm/sge/pbs/lsf) backend only.
# This is important for call-caching,
# which means re-using outputs from previous/failed workflows.
# Cache will miss if different strategy is used.
# "file" method has been default for all old versions of Caper<1.0.
# "path+modtime" is a new default for Caper>=1.0,
#   file: use md5sum hash (slow).
#   path: use path.
#   path+modtime: use path and modification time.
local-hash-strat=path+modtime

# Metadata DB for call-caching (reusing previous outputs):
# Cromwell supports restarting workflows based on a metadata DB
# DB is in-memory by default
#db=in-memory

# If you use 'caper server' then you can use one unified '--file-db'
# for all submitted workflows. In such case, uncomment the following two lines
# and defined file-db as an absolute path to store metadata of all workflows
#db=file
#file-db=

# If you use 'caper run' and want to use call-caching:
# Make sure to define different 'caper run ... --db file --file-db DB_PATH'
# for each pipeline run.
# But if you want to restart then define the same '--db file --file-db DB_PATH'
# then Caper will collect/re-use previous outputs without running the same task again
# Previous outputs will be simply hard/soft-linked.


# Local directory for localized files and Cromwell's intermediate files
# If not defined, Caper will make .caper_tmp/ on local-out-dir or CWD.
# /tmp is not recommended here since Caper store all localized data files
# on this directory (e.g. input FASTQs defined as URLs in input JSON).
local-loc-dir=/mnt/storage/hong/caper

cromwell=/home/hong/.caper/cromwell_jar/cromwell-65.jar
womtool=/home/hong/.caper/womtool_jar/womtool-65.jar

Input JSON file

{
  "wgbs.benchmark_mode": true,
  "wgbs.extra_reference": "tests/data/conversion_control.fa.gz",
  "wgbs.fastqs": [
    [
      [
        "tests/data/sample5_data_1_200000.fastq.gz",
        "tests/data/sample5_data_2_200000.fastq.gz"
      ]
    ]
  ],
  "wgbs.reference": "tests/data/sacCer3.fa.gz",
  "wgbs.sample_names": [
    "sample5"
  ],
  "wgbs.underconversion_sequence_name": "NC_001416.1"
}

Error log Caper automatically runs a troubleshooter for failed workflows. If it doesn't then get a WORKFLOW_ID of your failed workflow with caper list or directly use a metadata.json file on Caper's output directory.

* Found failures JSON object.
[
    {
        "message": "Workflow failed",
        "causedBy": [
            {
                "message": "Job wgbs.make_conf:NA:2 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.",
                "causedBy": []
            },
            {
                "message": "Job wgbs.make_metadata_csv:NA:2 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.",
                "causedBy": []
            }
        ]
    }
]
* Recursively finding failures in calls (tasks)...

==== NAME=wgbs.make_conf, STATUS=RetryableFailure, PARENT=
SHARD_IDX=-1, RC=1, JOB_ID=588529
START=2022-02-24T14:20:39.912Z, END=2022-02-24T14:20:52.057Z
STDOUT=/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_conf/execution/stdout
STDERR=/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_conf/execution/stderr
STDERR_CONTENTS=
/home/hong/anaconda3/envs/wgbs/bin/python3: can't find '__main__' module in '/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_conf/execution/'

STDERR_BACKGROUND_CONTENTS=
/home/hong/anaconda3/envs/wgbs/bin/python3: can't find '__main__' module in '/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_conf/execution/'



==== NAME=wgbs.make_conf, STATUS=Failed, PARENT=
SHARD_IDX=-1, RC=1, JOB_ID=592187
START=2022-02-24T14:20:54.103Z, END=2022-02-24T14:21:01.920Z
STDOUT=/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_conf/attempt-2/execution/stdout
STDERR=/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_conf/attempt-2/execution/stderr
STDERR_CONTENTS=
/home/hong/anaconda3/envs/wgbs/bin/python3: can't find '__main__' module in '/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_conf/attempt-2/execution/'

STDERR_BACKGROUND_CONTENTS=
/home/hong/anaconda3/envs/wgbs/bin/python3: can't find '__main__' module in '/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_conf/attempt-2/execution/'



==== NAME=wgbs.make_metadata_csv, STATUS=RetryableFailure, PARENT=
SHARD_IDX=-1, RC=1, JOB_ID=588545
START=2022-02-24T14:20:40.106Z, END=2022-02-24T14:20:52.057Z
STDOUT=/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_metadata_csv/execution/stdout
STDERR=/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_metadata_csv/execution/stderr
STDERR_CONTENTS=
/home/hong/anaconda3/envs/wgbs/bin/python3: can't find '__main__' module in '/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_metadata_csv/execution/'

STDERR_BACKGROUND_CONTENTS=
/home/hong/anaconda3/envs/wgbs/bin/python3: can't find '__main__' module in '/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_metadata_csv/execution/'



==== NAME=wgbs.make_metadata_csv, STATUS=Failed, PARENT=
SHARD_IDX=-1, RC=1, JOB_ID=593365
START=2022-02-24T14:20:56.102Z, END=2022-02-24T14:21:03.969Z
STDOUT=/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_metadata_csv/attempt-2/execution/stdout
STDERR=/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_metadata_csv/attempt-2/execution/stderr
STDERR_CONTENTS=
/home/hong/anaconda3/envs/wgbs/bin/python3: can't find '__main__' module in '/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_metadata_csv/attempt-2/execution/'

STDERR_BACKGROUND_CONTENTS=
/home/hong/anaconda3/envs/wgbs/bin/python3: can't find '__main__' module in '/home/hong/wgbs-pipeline/wgbs/9cd9270a-b1e7-45cb-a706-260cd3685f1c/call-make_metadata_csv/attempt-2/execution/'


2022-02-24 15:21:17,695|caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1
2022-02-24 15:21:17,695|caper.cli|ERROR| Check stdout in /home/hong/wgbs-pipeline/cromwell.out.3