VIBRANT PATH ERROR

[CynthiaChibani]

Description of the bug

Hey there, i am trying to run the pipeline but we are getting error at step 15

It seems that the path is not set up correctly here and I have no idea how to resolve this as the script is created automatically upon running the pipeline.

Command used and terminal output

[b3/c9d89b] VIROPROFILER:VIRCONTIGS_PRE    | 1 of 1, failed: 1 ✘
Command error:
  cat: VIBRANT_contigs: Is a directory
  cat: VIBRANT_log_run_contigs.log/VIBRANT_phages_contigs/contigs.phages_combined.fna: Not a directory

This is due to the following command (cat VIBRANT_contigs VIBRANT_log_run_contigs.log/), which is probably a bug as the input file is stored as
/work_beegfs/sunam162/viro/work/b3/c9d89b208746dc12ad8c7f06ef20e3/VIBRANT_contigs/VIBRANT_phages_contigs/contigs.phages_combined.fna

Problematic script:

$ cat /work_beegfs/sunam162/viro/work/b3/c9d89b208746dc12ad8c7f06ef20e3/.command.sh
#!/bin/bash -euo pipefail
cat VIBRANT_contigs VIBRANT_log_run_contigs.log/VIBRANT_phages_contigs/contigs.phages_combined.fna | seqkit fx2tab -n > vibrant_vcontigs.list
csvtk grep -t -r -f checkv_quality -p 'Complete|High-quality|Medium-quality|Low-quality' quality_summary.tsv | cut -f1 | sed 1d > checkv_vcontigs.list
cat virus_dvf.list checkv_vcontigs.list vibrant_vcontigs.list | sort -u > putative_vcontigs_pref1.list
seqkit grep -f putative_vcontigs_pref1.list contigs_nrclib.fasta > putative_vcontigs_pref1.fasta

Relevant files

No response

System information

No response

[rujinlong]

Hi Cynthia, did you modified the /work_beegfs/sunam162/viro/work/b3/c9d89b208746dc12ad8c7f06ef20e3/.command.sh script manually? The first cat command in this script should look like cat VIBRANT_contigs/VIBRANT_..., but yours missed an / after the VIBRANT_contigs folder. Could you please try to fix this by deleting the output of VIBRANT step, and rerun the pipeline?