whatshap error: Read name occurs more than twice in the input file

[A97paupic]

Description of the bug

Whenever I try to run the pipeline using a reduced revio fastq file as a test, I run into this error: Read name occurs more than twice in the input file. Up to that point I have not experienced any problems. Do you have idea what is going on, is there a way to get around this error?

Command used and terminal output

ERROR ~ Error executing process > 'FELLEN31_SKIERFE:SKIERFE:PHASING:WHATSHAP_PHASE (pr_001_001)'

Caused by:
  Process `FELLEN31_SKIERFE:SKIERFE:PHASING:WHATSHAP_PHASE (pr_001_001)` terminated with an error exit status (1)

Command executed:

  whatshap phase \
      --ignore-read-groups --indels --distrust-genotypes \
      -o pr_001_001.sorted.vcf.gz.phased.vcf \
      --reference GCA_000001405.15_GRCh38_no_alt_analysis_set_nochr.fna \
      pr_001_001.sorted.vcf.gz \
      pr_001_001.bam

  bgzip \
      -@ 2 \
      pr_001_001.sorted.vcf.gz.phased.vcf

  tabix \
      -p vcf \
      pr_001_001.sorted.vcf.gz.phased.vcf.gz

  cat <<-END_VERSIONS > versions.yml
  "FELLEN31_SKIERFE:SKIERFE:PHASING:WHATSHAP_PHASE":
      whatshap: $( whatshap --version )
      bgzip: $( bgzip --version | head -n 1 | sed 's/bgzip (htslib) //g')
      tabix: $( tabix --version | head -n 1 | sed 's/tabix (htslib) //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Ignoring --row-limit as heuristic is not used as algorithm.
  WARNING: Ignoring --indels as indel phasing is default in WhatsHap 2.0+
  This is WhatsHap 2.2 running under Python 3.9.18
  [E::idx_find_and_load] Could not retrieve index file for 'pr_001_001.sorted.vcf.gz'
  [E::idx_find_and_load] Could not retrieve index file for 'pr_001_001.sorted.vcf.gz'
  [E::idx_find_and_load] Could not retrieve index file for 'pr_001_001.sorted.vcf.gz'
  Working on 1 sample from 1 family

  # Working on contig 1 in individual pr_001_001
  Found 6443 usable heterozygous variants (3298 skipped due to missing genotypes)
  ERROR: whatshap error: Read name 'm84045_230420_150058_s1/198967705/ccs' occurs more than twice in the input file

Relevant files

No response

System information

Nextflow v.23.04.2,
HPC,
slurm,
Singularity,
CentOS Linux,
fellen31/skierfe v1.0dev

[fellen31]

Hi,

Could you double check if you have multiple copies of this read in your input file? For example with:

zgrep -c "m84045_230420_150058_s1/198967705/ccs" REVIO_TEST_DATA.fastq.gz

[A97paupic]

Ah, it sure was one to many copies in the fastq file! It has been rectified and now it runs through the whatshap process as it should, thanks!

Regards,
Paul

[fellen31]

Nice to hear you could fix it!
Currently been working on adding test profile and data to make the pipeline easier to test and set up.

Just let me know if you encounter any more problems.
Felix