Closed cedwardson4 closed 1 month ago
Ah good intuition, the mash support was added recently to the module/pipeline and so hasn't been tested much.
Both @maxibor (who iirc updated the module) and myself are traveling but will look next week when back :)
OK I've semi-replicated but with mv: can't rename 'align/*': No such file or directory
in my case! So regardless that module appearsto be flakey in a variety of ways
Sounds like a find
or a if [[ -f something ]]; then
would do the trick
Done in the previous PRs listed aboev :)
Description of the bug
Process
NFCORE_MAG:MAG:GTDBTK:GTDBTK_CLASSIFYWF (SPAdes-MaxBin2-prokarya-unrefined-FF07295009)
terminated with an error exit status (1).Command "mv identify/ .", which errors with: "mv: can't rename 'identify/': No such file or directory"
I believe this is due to all genomes in the set classified with ANI pre-screening and thus no Identify or Align steps are performed, leading to no folder creation for those steps.
[2024-02-29 15:58:13] INFO: 18 genome(s) have been classified using the ANI pre-screening step. [2024-02-29 15:58:13] INFO: Done. [2024-02-29 15:58:13] INFO: All genomes have been classified by the ANI screening step, Identify and Align steps will be skipped.
Command used and terminal output
Relevant files
nextflow.log
System information
Nextflow version: 23.10.1.5891 Hardware: Desktop Executor: local Container engine: Docker OS: Ubuntu 22.04.4 LTS Version of nf-core/mag: 2.5.4