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EBI-Metagenomics / genomes-catalogue-pipeline

MGnify genome analysis pipeline
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KRAKEN2_BUILD cp *.txt permission error #84

Open akques opened 11 months ago

akques commented 11 months ago

Hi, I might an error in Process: GAP:KRAKEN_SWF:KRAKEN2_BUILD (1).

ERROR~ Error executing process > 'GAP:KRAKEN_SWF:KRAKEN2_BUILD (1)'

Caused by:
  Process `GAP:KRAKEN_SWF:KRAKEN2_BUILD (1)` terminated with an error exit status (1)

Command executed:

  kraken2-build --build     --db kraken2_db_zebrafish-faecal_v1.0     --threads 1

Command exit status:
  1

Command output:
  (empty)

Command error:
  cp: cannot open '/mnt/02.program/10.mgnify_test/00.script_test/work/f1/41e40f8fb880a273d678abd448e214/kraken2_db_zebrafish-faecal_v1.0/library/added/prelim_map_Nyw1kzZg3u.txt' for reading: Permission denied
  cp: cannot open '/mnt/02.program/10.mgnify_test/00.script_test/work/f1/41e40f8fb880a273d678abd448e214/kraken2_db_zebrafish-faecal_v1.0/library/added/prelim_map_c3xTok5gdJ.txt' for reading: Permission denied
  cp: cannot open '/mnt/02.program/10.mgnify_test/00.script_test/work/f1/41e40f8fb880a273d678abd448e214/kraken2_db_zebrafish-faecal_v1.0/library/added/prelim_map_RIfYUEdjBD.txt' for reading: Permission denied

Work dir:
  /mnt/02.program/10.mgnify_test/00.script_test/work/a4/3db458ad6a66b51a0da32baa40ae28

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

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!

drwxr-xr-x 2 root root    4096 Dec 26 15:11 ./
drwxr-xr-x 3 root root    4096 Dec 26 15:11 ../
-rw-r--r-- 1 root root 2317728 Dec 26 15:11 GNBKq8t8Va.fna
-rw-r--r-- 1 root root       0 Dec 26 15:11 GNBKq8t8Va.fna.masked
-rw-r--r-- 1 root root 2281926 Dec 26 15:11 M1kPl0XaQL.fna
-rw-r--r-- 1 root root       0 Dec 26 15:11 M1kPl0XaQL.fna.masked
-rw-r--r-- 1 root root 1769393 Dec 26 15:11 jMxWgZVgaq.fna
-rw-r--r-- 1 root root       0 Dec 26 15:11 jMxWgZVgaq.fna.masked
-rw------- 1 root root    1071 Dec 26 15:11 prelim_map_Nyw1kzZg3u.txt
-rw------- 1 root root    1041 Dec 26 15:11 prelim_map_RIfYUEdjBD.txt
-rw------- 1 root root    3603 Dec 26 15:11 prelim_map_c3xTok5gdJ.txt

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)

akques commented 11 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
mberacochea commented 10 months ago

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