While running nohup caper run chip.wdl -i https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI_subsampled_chr19_only.json --conda &
I got error as: Conda environment name not found in WDL metadata. and caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1 and a cromwell.out with nothing in it.
I tried to follow issue #271 to remove and re-install caper and conda_env, but still get the same output.
OS/Platform
OS/Platform: CentOS 7.5.1804
Conda version: conda 23.1.0
Pipeline version: v2.2.1
Caper version: v2.2.3
Caper configuration file
Paste contents of ~/.caper/default.conf.
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/encode-dcc
cromwell=/home/.caper/cromwell_jar/cromwell-82.jar
womtool=/home/.caper/womtool_jar/womtool-82.jar
Input JSON file
Paste contents of your input JSON file.
{
"chip.pipeline_type" : "tf",
"chip.genome_tsv" : "https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v3/hg38_chr19_chrM.tsv",
"chip.fastqs_rep1_R1" : ["https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/rep1.subsampled.25.fastq.gz"
],
"chip.fastqs_rep2_R1" : ["https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/rep2.subsampled.20.fastq.gz"
],
"chip.ctl_fastqs_rep1_R1" : ["https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/ctl1.subsampled.25.fastq.gz"
],
"chip.ctl_fastqs_rep2_R1" : ["https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/ctl2.subsampled.25.fastq.gz"
],
"chip.paired_end" : false,
"chip.title" : "ENCSR000DYI (subsampled 1/25, chr19_chrM only)",
"chip.description" : "CEBPB ChIP-seq on human A549 produced by the Snyder lab"
}
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].
Describe the bug
While running
nohup caper run chip.wdl -i https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI_subsampled_chr19_only.json --conda &
I got error as:Conda environment name not found in WDL metadata.
andcaper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1
and a cromwell.out with nothing in it.I tried to follow issue #271 to remove and re-install caper and conda_env, but still get the same output.
OS/Platform
Caper configuration file
Paste contents of
~/.caper/default.conf
.Input JSON file
Paste contents of your input JSON file.
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) withcaper list
and runcaper debug [WORKFLOW_ID]
.Paste troubleshooting result.