Process `pipeline:getVersions` terminated with an error exit status (141)

[ineskozar]

I have encountered some inconsistencies when running the wf-artic pipeline. Sometimes the pipeline is running without any issues, wheres on other occasions I get the error below, which appears to be caused by a failed pipeline:getVersions, and I am not sure what is causing it?

Does anyone know what the issue could be?

Thanks a lot in advance.

$nextflow run epi2me-labs/wf-artic -w ${OUTPUT}/workspace -profile conda --fastq /path/to/reads/fastq_demultiplexed --samples /path/to/sample/sheet/sample_sheet --out_dir ${OUTPUT} N E X T F L O W ~ version 21.10.4 WARN: Access to undefined parameter detect_samples -- Initialise it to a default value eg. params.detect_samples = some_value Checking sample sheet. executor > local (8) [8d/de2916] process > checkSampleSheet (1) [100%] 1 of 1 ✔ executor > local (8) [8d/de2916] process > checkSampleSheet (1) [100%] 1 of 1 ✔ [88/63dc7b] process > pipeline:getVersions [100%] 1 of 1, failed: 1 ✘ [1a/bf87f8] process > pipeline:getParams [100%] 1 of 1 ✔ [35/7951d4] process > pipeline:copySchemeDir [100%] 1 of 1 ✔ [c4/64a846] process > pipeline:preArticQC (3) [ 0%] 0 of 1 [- ] process > pipeline:runArtic [ 0%] 0 of 5 [- ] process > pipeline:allConsensus - [- ] process > pipeline:allVariants - [- ] process > pipeline:nextclade - [- ] process > pipeline:pangolin - [- ] process > pipeline:telemetry - [- ] process > pipeline:report - [- ] process > output - Checking input directory structure.

• Found barcode directories Error executing process > 'pipeline:getVersions'

Caused by: Process pipeline:getVersions terminated with an error exit status (141)

Command executed:

medaka --version | sed 's/ /,/' >> versions.txt minimap2 --version | sed 's/^/minimap2,/' >> versions.txt bcftools --version | head -n 1 | sed 's/ /,/' >> versions.txt samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt nextclade --version | sed 's/^/nextclade,/' >> versions.txt artic --version | sed 's/ /,/' >> versions.txt

Command exit status: 141

Command output: (empty)

Work dir: ${OUTPUT}/workspace/88/63dc7bd7dd452b057b7b440902af74

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.

[sarahjeeeze]

I haven't been able to recreate this error but perhaps check you have the most up to date version with nextflow pull epi2me-labs/wf-artic