Dear all, With our latest batch of data, I was running into several

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This should have been fix in <a class="issue-link js-issue-link" data-error-text="Fail

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Problem masking the consensus sequence about viralrecon HOT 7 CLOSED

nf-core commented on June 15, 2024

Problem masking the consensus sequence

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Comments (7)

drpatelh commented on June 15, 2024 1

@saramonzon @svarona have you come across anything like this? What's the best fix?

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saramonzon commented on June 15, 2024 1

Yes, this is the fix included in dev, for bcftools consensus as varscan has been dropped!

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ktrns commented on June 15, 2024

Running viralrecon with --callers varscan2,ivar we get the following log:

Caused by:
  Process `VARSCAN2_CONSENSUS (Lib1)` terminated with an error exit status (2)

Command executed:

  cat MN908947_nCoV_2019_Wuhan.fa | bcftools consensus Lib1.AF0.75.vcf.gz > Lib1.AF0.75.consensus.fa
  
  bedtools genomecov \
      -bga \
      -ibam Lib1.trim.mkD.sorted.bam \
      -g MN908947_nCoV_2019_Wuhan.fa \
      | awk '$4 < 10' | bedtools merge > Lib1.AF0.75.mask.bed
  
  bedtools maskfasta \
      -fi Lib1.AF0.75.consensus.fa \
      -bed Lib1.AF0.75.mask.bed \
      -fo Lib1.AF0.75.consensus.masked.fa
  header=$(head -n 1 Lib1.AF0.75.consensus.masked.fa | sed 's/>//g')
  sed -i "s/${header}/Lib1/g" Lib1.AF0.75.consensus.masked.fa
  
  plot_base_density.r --fasta_files Lib1.AF0.75.consensus.masked.fa --prefixes Lib1.AF0.75 --output_dir ./

So it looks very similar.

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ktrns commented on June 15, 2024

It looks like the pipeline requires a liftOver at different places.

You can run bcftools consensus with --chain to write a chain file for liftOver, and then run liftOver for the *.mask.bed file.

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drpatelh commented on June 15, 2024

This should have been fix in #146. Be great if you can test the code on dev and close this issue if that's the case @ktrns 🙂 Apologies for the delay in getting around to merging.

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drpatelh commented on June 15, 2024

I assume this is now fixed @saramonzon?

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drpatelh commented on June 15, 2024

Ping @saramonzon

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