Troubleshooting - alesssia/YAMP GitHub Wiki

Here there is a list of known issues, with the hope that they will be helpful. Please report any issue using the GitHub platform.

  • If you get this error:

    Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.

    please decomment the following line: docker.runOptions = "--memory-swap '-1'" in the nextflow.config file. Thanks to Flavia Flaviani for identifying and solving this problem.

  • if you get this error:

    Command error:
Command 'ps' required by nextflow to collect task metrics cannot be found

    please ensure that trace, timeline, and report are set to falsein the nextflow.config file (default behaviour from version 0.9.5.2). Thanks to Guillaume Filion for pointing it out here.

  • if you get this or a similar error:

    Command error:
.command.sh: line 4: dedup_mqc.txt: Operation not permitted

    please uncheck Use gRPC FUSE for file sharing in your Docker Desktop app (Docker Desktop โ†’ Preferences โ†’ General) in order to use the legacy osxfs file sharing. This should happen only on MacOS when using Docker.

  • if the alpha_diversity process (qiime2) generates the following error:

    An unexpected error has occurred:
[Errno 17] File exists: '/tmp/q2-BIOMV210DirFmt-_5c_f1px' -> '/tmp/qiime2-archive-zn0r4jma/0bf95333-bd7f-4bd0-8726-645c0016e339/data'

    please create a local tmpdir and export it accordingly before running qiime2:

    export TMPDIR=/path/to/your/desired/local/tmp
mkdir $TMPDIR

    Thanks to Nadine for identifying and solving this problem here.

  • the --prefix option can't contain a #. If you use it, the pipeline will terminate early with no error message. Thanks to Will Rowe for pointing it out here.

  • When running on AWSbacth, YAMP may fail when reaching the alpha_diversity step due to a missing file, prompting the following message:

    Caused by:
  Can't stage file file:///efs/yamp/tests/batch/null -- file does not exist

    To solve this you should edit the YAMP.nf file as described here by Gil Freund, who found and fixed the issue. Thanks Gil!

Versions prior to 0.9.5

  • If you get this error:

    Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
touch: cannot touch โ€˜.command.traceโ€™: Permission denied

    please add docker.runOptions = '-u $(id -u):$(id -g)' in the nextflow.config file. Thanks to wangdatou2009 for pointing this out here.

  • if you are using the sequencing_artifacts.fa resources we made available through Zenodo, and a BBmap version higher than 37.52, please be aware that the contam_15 sequence contains a P char that your version of BBmap would not be able to process. To solve the issue you can either

    1. downgrade BBmap,
    2. substitute the sequencing_artifacts.fa file you found in the Zenodo archive with that made available with your (newest) BBmap version (you can find it in the BBmap archive, downloadable here),
    3. edit the sequencing_artifacts.fa file using the BBmap command fixjunk (or remove the offending P)

    Thanks to Will Rowe for pointing it out here