The bioBakery help forum

Docker image: outdated kneaddata?

Hello, I am running into issue with running docker image of Workflows in Singularity. When I run wmgx workflow (command singularity biobakery_workflows wmgx --input ./workflow_test/ --output ./workflow_test_out_sin/ --input-extension fastq --local-jobs 2 --threads 4), I get following error:

Err: b'usage: kneaddata [-h] [--version] [-v] -i INPUT -o OUTPUT_DIR\n                 [-db REFERENCE_DB] [--bypass-trim]\n                 [--output-prefix OUTPUT_PREFIX] [-t <1>] [-p <1>]\n                 [-q {phred33,phred64}] [--run-bmtagger] [--bypass-trf]\n                 [--run-fastqc-start] [--run-fastqc-end] [--store-temp-output]\n                 [--remove-intermediate-output] [--cat-final-output]\n                 [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--log LOG]\n                 [--trimmomatic TRIMMOMATIC_PATH] [--max-memory MAX_MEMORY]\n                 [--trimmomatic-options TRIMMOMATIC_OPTIONS]\n                 [--bypass-trim-repetitive] [--bowtie2 BOWTIE2_PATH]\n                 [--bowtie2-options BOWTIE2_OPTIONS] [--no-discordant]\n                 [--reorder] [--serial] [--bmtagger BMTAGGER_PATH]\n                 [--trf TRF_PATH] [--match MATCH] [--mismatch MISMATCH]\n                 [--delta DELTA] [--pm PM] [--pi PI] [--minscore MINSCORE]\n                 [--maxperiod MAXPERIOD] [--fastqc FASTQC_PATH]\nkneaddata: error: unrecognized arguments: --run-trf\n'

As far as I managed to find out, the ‘unrecognized arguments: --run-trf\n’ may be related to outdated kneaddata in the container (the latest container includes version Any feasible workarounds?

Also, is the dockerfile available anywhere? This would enable me to update the kneaddata by myself and I’d love try to prepare my own container, that would include the databases for kneaddata and maybe a custom database further down the line.

P.S. Full log of the failed run included.Processing: anadama.log…
anadama.txt (119.7 KB)

Hello, The latest docker image of the bioBakery workflows should include the kneaddata version that is in sync with the options.

Yes the Dockerfile is available in the biobakery repository in GitHub in the “docker/workflows” folder.

Thank you,

1 Like