#C07MFUQAR1B is giving the following error even though I prepared the

samplesheet.csv

as suggested. Merging the (u)BAM fix the problem or what could be the solution to this problem?

nf-core/pacvar execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'NFCORE_PACVAR:PACVAR:PBMM2_ALIGN (F2)'

Caused by:
  Process `NFCORE_PACVAR:PACVAR:PBMM2_ALIGN (F2)` terminated with an error exit status (1)


Command executed:

  # pbmm2 doesn't support .fna extension, so rename to .fa
  if [[ WIK.fasta == *.fna ]]; then
      ln -s $(readlink -f WIK.fasta) ${WIK.fasta‰.fna}.fa
  elif [[ WIK.fasta == *.fna.gz ]]; then
      ln -s $(readlink -f WIK.fasta) ${WIK.fasta‰.fna.gz}.fa.gz
  fi

  pbmm2 \
      align \
       \
      WIK.fasta \
      m54313U_230812_104833.hifi_reads.bam m54313U_230813_201738.hifi_reads.bam m54313U_230815_054336.hifi_reads.bam m64467e_231012_162531.hifi_reads.bam m64467e_231014_031918.hifi_reads.bam m64467e_231028_115954.hifi_reads.bam m64467e_231029_225641.hifi_reads.bam m64467e_231109_162002.hifi_reads.bam m64467e_231111_031411.hifi_reads.bam m64467e_231215_162529.hifi_reads.bam m64467e_231217_015127.hifi_reads.bam m64467e_231218_112251.hifi_reads.bam m64467e_231219_210103.hifi_reads.bam m64467e_240621_234540.hifi_reads.bam m64467e_240623_091000.hifi_reads.bam \
      F2.aligned.bam \
      --num-threads 12

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_PACVAR:PACVAR:PBMM2_ALIGN":
      pbmm2: $(pbmm2 --version |& sed '1!d ; s/pbmm2 //')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Not virtualizing pid namespace by configuration
  >|> 20260617 21:52:19.792 -|- FATAL -|- CheckPositionalArgs -|- 0x155555254040|| -|- pbmm2 align ERROR: Incorrect number of arguments. Accepted are at most three!

Work dir:
  /vf/users/recombination/claudia_recomb_2/results/alignments/WIK/work/ca/561b01d4adf8479672063f0977b3aa

Container:
  /data/nxf_singularity_cache/depot.galaxyproject.org-singularity-pbmm2-1.14.99--h9ee0642_0.img

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

The right place for this question is #C07MFUQAR1B. Do all these BAM files belong to the same sample? If so, I suspect this pipeline may not currently be able to deal with more than one BAM per sample, but this is not reflected in the sample sheet validation. If this is indeed the case, I would merge (e.g. with

samtools merge

) all the BAMs for one sample into one BAM file and then put that into the sample sheet. If the BAMs represent different samples, make sure the

sample

column in the CSV has a unique value for each. In any case, I would bring this up in the #C07MFUQAR1B channel, so that the developers can see it and take the appropriate steps (clarify documentation, fix any bugs, etc.).

The pipeline indeed accounts for multiple bam files per sample and groups them correctly. However, the nf-core pbmm2 module is not able to handle input from multiple bam files. So this is is bug in the pipeline. It would be easy to modify the module in a way that if with

bam.size() > 1

, file names are written into a fofn instead.

The BAM belongs to a single individual. I will merge them then retry the pipeline

But please report it to the pacvar developers. This is a common use case.