metabat2 "[Error!] the order of contigs in abundance file is not the same as the assembly file"

[nf-core]

metabat2 "[Error!] the order of contigs in abundance file is not the same as the assembly file"

[d4straub]

Thanks a lot for your feedback!

For fixing this immediately, you can try running your command appending -c quast.config -resume where quast.config contains:

process {
  withName: quast_bins {
    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
  }
}

However, this is a deeper problem obviously: The files SPAdes-mock_first.lowDepth.fa SPAdes-mock_first.tooShort.fa SPAdes-mock_first.unbinned.pooled.fa are not supposed to be processed by this process.
This might be an issue of a recent change, could you please provide what exact commit you used?

@skrakau might that be an issue that needs to be resolved or is it already solved?

[d4straub]

Thanks and sorry, I was not clear. What I meant was "revision" info, here:

N E X T F L O W  ~  version 20.01.0
Launching `d4straub/mag` [spontaneous_hopper] - revision: f0206789cc [d4straub-v0.2-exportDepth]
[2m----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/mag v1.0.0
----------------------------------------------------

or commit hash in results/pipeline_info/execution_report.html:

Workflow repository
    https://github.com/d4straub/mag.git, revision d4straub-v0.2-exportDepth (commit hash f0206789cccf699e69652f0223e2148f7c1f6ea7)

This is to dentify what version/revision/commit of dev you used to then judge whether this might have been fixed already.

[d4straub]

Please have a look at #32 , thats the identical issue.
Problem can be solved by either (1) resume the pipeline with -resume, that seems to help usually or (2) use the dev branch (-r dev), there is a fix.

I close here cause its a duplicate.

[jfourquet2]

Thanks a lot !

[jfourquet2]

For information, I re-run my initial script with mag 1.0.0 (and not dev version) and it works well with nfcore-Nextflow-v20.01.0 (I ran my previous script with nfcore-Nextflow-v19.04.0).
The run with dev version and nfcore-Nextflow-v19.04.0 finished with an error :

ERROR ~ Error executing process > 'quast_bins (SPAdes-mock_first)'

Caused by:
  Process `quast_bins (SPAdes-mock_first)` terminated with an error exit status (4)

Command executed:

  ASSEMBLIES=$(echo "SPAdes-mock_first.1.fa SPAdes-mock_first.10.fa SPAdes-mock_first.11.fa SPAdes-mock_first.12.fa SPAdes-mock_first.13.fa SPAdes-mock_first.14.fa SPAdes-mock_first.15.fa SPAdes-mock_first.16.fa SPAdes-mock_first.17.fa SPAdes-mock_first.18.fa SPAdes-mock_first.19.fa SPAdes-mock_first.2.fa SPAdes-mock_first.20.fa SPAdes-mock_first.21.fa SPAdes-mock_first.22.fa SPAdes-mock_first.23.fa SPAdes-mock_first.24.fa SPAdes-mock_first.25.fa SPAdes-mock_first.26.fa SPAdes-mock_first.27.fa SPAdes-mock_first.28.fa SPAdes-mock_first.29.fa SPAdes-mock_first.3.fa SPAdes-mock_first.30.fa SPAdes-mock_first.31.fa SPAdes-mock_first.32.fa SPAdes-mock_first.33.fa SPAdes-mock_first.34.fa SPAdes-mock_first.35.fa SPAdes-mock_first.36.fa SPAdes-mock_first.37.fa SPAdes-mock_first.38.fa SPAdes-mock_first.39.fa SPAdes-mock_first.4.fa SPAdes-mock_first.40.fa SPAdes-mock_first.5.fa SPAdes-mock_first.6.fa SPAdes-mock_first.7.fa SPAdes-mock_first.8.fa SPAdes-mock_first.9.fa SPAdes-mock_first.lowDepth.fa SPAdes-mock_first.tooShort.fa SPAdes-mock_first.unbinned.pooled.fa" | sed 's/[][]//g')
  IFS=', ' read -r -a assemblies <<< "$ASSEMBLIES"
  
  for assembly in "${assemblies[@]}"; do
      metaquast.py --threads "1" --max-ref-number 0 --rna-finding --gene-finding -l "${assembly}" "${assembly}" -o "QUAST/${assembly}"
      if ! [ -f "QUAST/SPAdes-mock_first-quast_summary.tsv" ]; then 
          cp "QUAST/${assembly}/transposed_report.tsv" "QUAST/SPAdes-mock_first-quast_summary.tsv"
      else
          tail -n +2 "QUAST/${assembly}/transposed_report.tsv" >> "QUAST/SPAdes-mock_first-quast_summary.tsv"
      fi
  done

Command exit status:
  4

Command output:
  
  NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
  
  2020-07-01 09:00:35
  Running Barrnap...
  Logging to QUAST/SPAdes-mock_first.9.fa/predicted_genes/barrnap.log...
      Ribosomal RNA genes = 0
      Predicted genes (GFF): QUAST/SPAdes-mock_first.9.fa/predicted_genes/SPAdes-mock_first-9-fa.rna.gff
  Done.
  
  2020-07-01 09:00:39
  Creating large visual summaries...
  This may take a while: press Ctrl-C to skip this step..
    1 of 2: Creating Icarus viewers...
    2 of 2: Creating PDF with all tables and plots...
  Done
  
  2020-07-01 09:00:39
  RESULTS:
    Text versions of total report are saved to QUAST/SPAdes-mock_first.9.fa/report.txt, report.tsv, and report.tex
    Text versions of transposed total report are saved to QUAST/SPAdes-mock_first.9.fa/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
    HTML version (interactive tables and plots) is saved to QUAST/SPAdes-mock_first.9.fa/report.html
    PDF version (tables and plots) is saved to QUAST/SPAdes-mock_first.9.fa/report.pdf
    Icarus (contig browser) is saved to QUAST/SPAdes-mock_first.9.fa/icarus.html
    Log is saved to QUAST/SPAdes-mock_first.9.fa/quast.log
  
  Finished: 2020-07-01 09:00:39
  Elapsed time: 0:00:05.786084
  NOTICEs: 2; WARNINGs: 2; non-fatal ERRORs: 0
  
  Thank you for using QUAST!
  /opt/conda/envs/nf-core-mag-1.1.0dev/lib/python3.6/site-packages/quast-5.0.2-py3.6.egg-info/scripts/metaquast.py --threads 1 --max-ref-number 0 --rna-finding --gene-finding -l SPAdes-mock_first.lowDepth.fa SPAdes-mock_first.lowDepth.fa -o QUAST/SPAdes-mock_first.lowDepth.fa
  
  Version: 5.0.2
  
  System information:
    OS: Linux-3.10.0-514.26.2.el7.x86_64-x86_64-with-debian-10.1 (linux_64)
    Python version: 3.6.7
    CPUs number: 64
  
  Started: 2020-07-01 09:00:39
  
  Logging to QUAST/SPAdes-mock_first.lowDepth.fa/metaquast.log
  
  Contigs:
    Pre-processing...
  WARNING: Skipping SPAdes-mock_first.lowDepth.fa because it doesn't contain contigs >= 0 bp.
  
  
  ERROR! None of the assembly files contains correct contigs. Please, provide different files or decrease --min-contig threshold.

Command wrapper:
  
  NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
  
  2020-07-01 09:00:35
  Running Barrnap...
  Logging to QUAST/SPAdes-mock_first.9.fa/predicted_genes/barrnap.log...
      Ribosomal RNA genes = 0
      Predicted genes (GFF): QUAST/SPAdes-mock_first.9.fa/predicted_genes/SPAdes-mock_first-9-fa.rna.gff
  Done.
  
  2020-07-01 09:00:39
  Creating large visual summaries...
  This may take a while: press Ctrl-C to skip this step..
    1 of 2: Creating Icarus viewers...
    2 of 2: Creating PDF with all tables and plots...
  Done
  
  2020-07-01 09:00:39
  RESULTS:
    Text versions of total report are saved to QUAST/SPAdes-mock_first.9.fa/report.txt, report.tsv, and report.tex
    Text versions of transposed total report are saved to QUAST/SPAdes-mock_first.9.fa/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
    HTML version (interactive tables and plots) is saved to QUAST/SPAdes-mock_first.9.fa/report.html
    PDF version (tables and plots) is saved to QUAST/SPAdes-mock_first.9.fa/report.pdf
    Icarus (contig browser) is saved to QUAST/SPAdes-mock_first.9.fa/icarus.html
    Log is saved to QUAST/SPAdes-mock_first.9.fa/quast.log
  
  Finished: 2020-07-01 09:00:39
  Elapsed time: 0:00:05.786084
  NOTICEs: 2; WARNINGs: 2; non-fatal ERRORs: 0
  
  Thank you for using QUAST!
  /opt/conda/envs/nf-core-mag-1.1.0dev/lib/python3.6/site-packages/quast-5.0.2-py3.6.egg-info/scripts/metaquast.py --threads 1 --max-ref-number 0 --rna-finding --gene-finding -l SPAdes-mock_first.lowDepth.fa SPAdes-mock_first.lowDepth.fa -o QUAST/SPAdes-mock_first.lowDepth.fa
  
  Version: 5.0.2
  
  System information:
    OS: Linux-3.10.0-514.26.2.el7.x86_64-x86_64-with-debian-10.1 (linux_64)
    Python version: 3.6.7
    CPUs number: 64
  
  Started: 2020-07-01 09:00:39
  
  Logging to QUAST/SPAdes-mock_first.lowDepth.fa/metaquast.log
  
  Contigs:
    Pre-processing...
  WARNING: Skipping SPAdes-mock_first.lowDepth.fa because it doesn't contain contigs >= 0 bp.
  
  
  ERROR! None of the assembly files contains correct contigs. Please, provide different files or decrease --min-contig threshold.

I will re-run the dev versin with nfcore-Nextflow-v20.01.0 and I think it will be ok !

[jfourquet2]

Thanks for your answer !
My command line was:

nextflow run nf-core/mag -profile genotoul --reads '../mag/*_R{1,2}.fastq.gz' --busco_reference '/work2/g
enphyse/NED_metaG/src/mag/bacteria_odb9.tar.gz' --kraken2_db '/work2/genphyse/NED_metaG/src/mag/minikrake
n2_v2_8GB_201904_UPDATE.tgz' --centrifuge_db '/work2/genphyse/NED_metaG/src/mag/p_compressed+h+v.tar.gz' 
--cat_db '/work2/genphyse/NED_metaG/src/mag/CAT_prepare_20190108.tar.gz' -with-timeline -with-trace -with
-report -with-dag -r dev

And in software_versions.csv there is all tools and versions of tools (and version of mag dev):

nf-core/mag	v1.1.0dev
Nextflow	v19.04.0
MultiQC	v1.9
FastQC	v0.11.8
fastp	v0.20.0
MEGAHIT	v1.2.7
Metabat	v2:2.15
NanoPlot	v1.26.3
Filtlong	v0.2.0
Porechop	v0.2.3_seqan2.1.1

[jfourquet2]

It was very clear but I didn't know how to have the number of the commit, thanks for your answer !
Workflow repository
https://github.com/nf-core/mag.git, revision dev (commit hash 973f8d4)

[skrakau]

Hi, the problem regarding the *.lowDepth.fa file was introduced with the new MetBAT2 version 2.15, and solved in commit 60cd556

[jfourquet2]

Ok, thanks a lot !

[skrakau]

Thanks for reporting @jfourquet2. I will close this, let us know if a problem remains.