BUSCO update

[nf-core]

BUSCO update

[d4straub]

If all possibilities would be implemented, I'd think the most requested cases would be --lineage_dataset bacteria_odb10 >> --auto-lineage > --lineage_dataset archea_odb10 > anything else. This is because usually the majority of genomes are bacteria and BUSCO evaluation results are best comparable if all bins are evaluated with the same reference data. Therefore, only making a single db available for now would be sufficient, I think. But the --auto-lineage option looks so tempting ;)

[skrakau]

UPDATE:

With BUSCO version 4.0.6 there are frequent, non-reproducible errors occurring, caused by a replace("faa", "fna") function corrupting nextflow filenames that contain the substring "faa" in their hash id. I prepared a fix for BUSCO (https://gitlab.com/ezlab/busco/-/issues/305). Waiting currently.

We need a new BUSCO release before preparing pipeline release.

[ropolomx]

Hi @skrakau . Are you referring to this type of error? I am getting a lot of these with BUSCO version 3.0.2when running mag with revision: 8586c49 [dev]

Aug-26 20:41:52.612 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'busco (MEGAHIT-SRR9030455.61.fa)'

Caused by:
  Process `busco (MEGAHIT-SRR9030455.61.fa)` terminated with an error exit status (1)

Command executed:

  run_BUSCO.py             --in MEGAHIT-SRR9030455.61.fa             --lineage_path bacteria_odb9             --cpu "4"             --blast_single_core             --mode genome             --out MEGAHIT-SRR9030455.61.fa             >MEGAHIT-SRR9030455.61.fa_busco_log.txt
  cp run_MEGAHIT-SRR9030455.61.fa/short_summary_MEGAHIT-SRR9030455.61.fa.txt short_summary_MEGAHIT-SRR9030455.61.fa.txt

  for f in run_MEGAHIT-SRR9030455.61.fa/single_copy_busco_sequences/*faa; do
      [ -e "$f" ] && cat run_MEGAHIT-SRR9030455.61.fa/single_copy_busco_sequences/*faa >MEGAHIT-SRR9030455.61.fa_buscos.faa || touch MEGAHIT-SRR9030455.61.fa_buscos.faa
      break
  done
  for f in run_MEGAHIT-SRR9030455.61.fa/single_copy_busco_sequences/*fna; do
      [ -e "$f" ] && cat run_MEGAHIT-SRR9030455.61.fa/single_copy_busco_sequences/*fna >MEGAHIT-SRR9030455.61.fa_buscos.fna || touch MEGAHIT-SRR9030455.61.fa_buscos.fna
      break
  done

Command exit status:
  1

Command output:
  (empty)

Command error:
  cp: cannot stat ‘run_MEGAHIT-SRR9030455.61.fa/short_summary_MEGAHIT-SRR9030455.61.fa.txt’: No such file or directory

[skrakau]

Hi @ropolomx, to be precise, the problem I described was for BUSCO 4 versions, which prevented us from updating BUSCO to solve some issues. But in BUSCO 3.0.2 there was a related problem, which can cause such errors as you described above (BUSCO itself did not return an error, but since an output file is missing, the downstream cp command failed).

[skrakau]

Solved in #103 :)