So I got the the DAS_tool contig2bin and my extended version of the same file implemented here: https://github.com/nf-core/mag/pull/965 When I run

nf-test

locally it runs fine with no error, but I'm getting snapshot differences: b ut I don't know why 😞 https://github.com/nf-core/mag/actions/runs/20854536246/job/59917663204?pr=965#step:4:944 It almost looks like to me like slight variation in the bins that are being output, but I don't know why that would be :\ Any suggestions?

Do you get the same issue a second time if you re-trigger the CI tests?

I think so, as I pushed a commit and same issue but will re-run now just to double check (and then can compare the two)

There are definitely issues in general with the binners being stochastic in what they output. But I don't see why the changes you've made would materially change anything coming out the binners/going in to DAS Tool

Yeah precisely, that was what has surprised me

Are the various reproduciblity options all set? metabat_rng seed etc.?

Aha...

I’m running your branch now. The thing that seems more odd to me the different process count (294 vs. 296). Do you know what those processes are?

Nope...

Fails for me

Whaaaat

Weird. In what environment are you running the tests? docker or apptainer? linux?

docker ubuntu locally

Give me your bin_summary too

bin_summary(1).tsv

and the execution timeline too

execution_timeline_2026-01-12_11-47-12.html

It seems that it's semibin

It's not executing on me and codspaces right?

For you semibin produces 2+1 bins, for me 2+2

That's what the only thing I didn't really recognise but I don't know why

image.png,image.png

We still test it in

test_hybrid

Ok, let's skip it then.

OK I'll push that

Sure, merge it!

Thank you!

Hej! Is it something similar that you are fixing? It is not working for any of my samples (V5.3) Workflow execution completed unsuccessfully The exit status of the task that caused the workflow execution to fail was:

1

Error executing process > 'NFCORE_MAG:MAG:BINNING_REFINEMENT:RENAME_PREDASTOOL (MEGAHIT-MetaBAT2-MMBO_02)'

Caused by:
  Process `NFCORE_MAG:MAG:BINNING_REFINEMENT:RENAME_PREDASTOOL (MEGAHIT-MetaBAT2-MMBO_02)` terminated with an error exit status (1)


Command executed:

  if [ -n "MEGAHIT-MetaBAT2-MMBO_02.1.fa MEGAHIT-MMBO_02.contigs.fa MEGAHIT-MetaBAT2-MMBO_02.10.fa MEGAHIT-MetaBAT2-MMBO_02.4.fa MEGAHIT-MetaBAT2-MMBO_02.2.fa MEGAHIT-MetaBAT2-MMBO_02.3.fa MEGAHIT-MetaBAT2-MMBO_02.11.fa MEGAHIT-MetaBAT2-MMBO_02.12.fa MEGAHIT-MetaBAT2-MMBO_02.5.fa MEGAHIT-MetaBAT2-MMBO_02.6.fa MEGAHIT-MetaBAT2-MMBO_02.7.fa MEGAHIT-MetaBAT2-MMBO_02.9.fa MEGAHIT-MetaBAT2-MMBO_02.8.fa" ]
  then
      for bin in MEGAHIT-MetaBAT2-MMBO_02.1.fa MEGAHIT-MMBO_02.contigs.fa MEGAHIT-MetaBAT2-MMBO_02.10.fa MEGAHIT-MetaBAT2-MMBO_02.4.fa MEGAHIT-MetaBAT2-MMBO_02.2.fa MEGAHIT-MetaBAT2-MMBO_02.3.fa MEGAHIT-MetaBAT2-MMBO_02.11.fa MEGAHIT-MetaBAT2-MMBO_02.12.fa MEGAHIT-MetaBAT2-MMBO_02.5.fa MEGAHIT-MetaBAT2-MMBO_02.6.fa MEGAHIT-MetaBAT2-MMBO_02.7.fa MEGAHIT-MetaBAT2-MMBO_02.9.fa MEGAHIT-MetaBAT2-MMBO_02.8.fa; do
          if [[ ${bin} =~ MEGAHIT-MetaBAT2-MMBO_02.([_[:alnum:]]+).fa ]]; then
              num=${BASH_REMATCH[1]}
              mv ${bin} MEGAHIT-MetaBAT2Refined-MMBO_02.${num}.fa
          else
              echo "ERROR: the bin filename ${bin} does not match the expected format 'MEGAHIT-MetaBAT2-MMBO_02.([_[:alnum:]]+).fa'!"
              exit 1
          fi
      done
  fi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_MAG:MAG:BINNING_REFINEMENT:RENAME_PREDASTOOL":
      coreutils: $(echo $(mv --version 2>&1) | sed 's/^.*(GNU coreutils) //; s/ Copyright.*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  ERROR: the bin filename MEGAHIT-MMBO_02.contigs.fa does not match the expected format 'MEGAHIT-MetaBAT2-MMBO_02.([_[:alnum:]]+).fa'!

@Juliana Assis no, your error is completely different... That's a new one!