Open akques opened 8 months ago
I'm not sure whether it relate to this bug https://github.com/nextflow-io/nextflow/issues/4565 ,but when I checked .command.error,I met this
/media/pipeline/anaconda3/envs/nextflow/.nextflow/assets/EBI-Metagenomics/genomes-pipeline/bin/gtdbToTaxonomy.pl Loaded 3 fasta files into the index
/media/pipeline/anaconda3/envs/nextflow/.nextflow/assets/EBI-Metagenomics/genomes-pipeline/bin/gtdbToTaxonomy.pl Loading MGYG000000000, d__Archaea;p__Thermo...A;s__Methanomassiliicoccus_A sp905202485
/media/pipeline/anaconda3/envs/nextflow/.nextflow/assets/EBI-Metagenomics/genomes-pipeline/bin/gtdbToTaxonomy.pl finding it (MGYG000000000)...got it!
/media/pipeline/anaconda3/envs/nextflow/.nextflow/assets/EBI-Metagenomics/genomes-pipeline/bin/gtdbToTaxonomy.pl Loading MGYG000000002, d__Bacteria;p__Actin...ifidobacterium;s__Bifidobacterium longum
/media/pipeline/anaconda3/envs/nextflow/.nextflow/assets/EBI-Metagenomics/genomes-pipeline/bin/gtdbToTaxonomy.pl finding it (MGYG000000002)...got it!
/media/pipeline/anaconda3/envs/nextflow/.nextflow/assets/EBI-Metagenomics/genomes-pipeline/bin/gtdbToTaxonomy.pl Loading MGYG000000004, d__Bacteria;p__Actin...aceae;g__Rothia;s__Rothia mucilaginosa_B
/media/pipeline/anaconda3/envs/nextflow/.nextflow/assets/EBI-Metagenomics/genomes-pipeline/bin/gtdbToTaxonomy.pl finding it (MGYG000000004)...got it!
chown: unrecognized option '--from'
BusyBox v1.32.1 (2021-04-13 11:15:36 UTC) multi-call binary.
Usage: chown [-RhLHPcvf]... USER[:[GRP]] FILE...
Change the owner and/or group of each FILE to USER and/or GRP
-R Recurse
-h Affect symlinks instead of symlink targets
-L Traverse all symlinks to directories
-H Traverse symlinks on command line only
-P Don't traverse symlinks (default)
-c List changed files
-v List all files
-f Hide errors
Hi @akques
Thank you for reporting this. You are correct, it's related to 4565 because the container is using BusyBox as the base image.
We will patch the container, but I don't have an ETA for this.
Cheers
Hi, I might an error in Process: GAP:KRAKEN_SWF:KRAKEN2_BUILD (1).
Then I changed the directory to the mentioned folder above. I checked these *txt files and observed their permissions, but I'm uncertain about the specific step in which these files were generated. Hope to receive some guidance!
Environment Nextflow version: 23.04.1 Java version: 17 Operating system: Linux Bash version: GNU bash, version 4.3.48(1)-release (x86_64-pc-linux-gnu)