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[question] Snippy failing when aligning to subset of reference #613

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[question] Snippy failing when aligning to subset of reference#613
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@nmmahmed

Description

@nmmahmed
nmmahmed
opened on Apr 15, 2025

Hi,

I ran bactopia on ~30 bacterial samples

bactopia --samples acc.txt --cleanup_workdir --outdir results --max_cpus 36 --max_time 240h --min_time 15000 --nfconfig config.nf -resume

I then ran it on two additional whole genomes which were stored locally. Both processes ran smoothly.

Next, I'm trying to use bactopia/snippy to align to a reference only containing only one of two chromosomes (though the initial sequence data I'm working from contains both chromosomes).

bactopia --wf snippy --mapqual 60 --basequal 13 --mincov 4 --minfrac .75  --bactopia results --reference chr1.gb --max_cpus 36 --max_time 240h --min_time 15000 --nfconfig config.nf --skip_recombination

This fails when executed. However, the same command runs smoothly when working with the reference containing both chromosomes.

Error log:

executor >  local (89)
[98/3a8e82] process > BACTOPIATOOLS:SNIPPY:SNIPPY... [ 75%] 87 of 116, failed...
[-        ] process > BACTOPIATOOLS:SNIPPY:SNIPPY... -
[-        ] process > BACTOPIATOOLS:SNIPPY:SNPDIS... -
[-        ] process > BACTOPIATOOLS:SNIPPY:IQTREE... -
[-        ] process > BACTOPIATOOLS:CUSTOM_DUMPSO... -

ERROR ~ Error executing process > 'BACTOPIATOOLS:SNIPPY:SNIPPY_RUN_MODULE (ERX1940103 - chr1)'

Caused by:
  Process `BACTOPIATOOLS:SNIPPY:SNIPPY_RUN_MODULE (ERX1940103 - chr1)` terminated with an error exit status (1)

Command executed:

  if [ "false" == "true" ]; then
      gzip -c -d chr1.gb > chr1.gb
  fi
  
  if ! head -n 1 chr1.gb | grep "^LOCUS"; then
      echo "ERROR: Reference file (chr1.gb) does not appear to be a GenBank file"
      exit 1
  fi
  
  mkdir tmp_snippy/
  snippy \
      --mapqual 60 --basequal 13 --mincov 4 --minfrac .75 --minqual 100 --maxsoft 10 \
      --cpus 36 \
      --outdir ERX1940103 \
      --reference chr1.gb \
      --prefix ERX1940103 \
      --tmpdir tmp_snippy/ \
      --R1 ERX1940103_R1.fastq.gz --R2 ERX1940103_R2.fastq.gz
  
  # Add GenBank annotations
  vcf-annotator ERX1940103/ERX1940103.vcf chr1.gb > ERX1940103/ERX1940103.annotated.vcf
  
  # Get per-base coverage
  grep "^##contig" ERX1940103/ERX1940103.vcf > ERX1940103/ERX1940103.full-coverage.txt
  genomeCoverageBed -ibam ERX1940103/ERX1940103.bam -d >> ERX1940103/ERX1940103.full-coverage.txt
  cleanup-coverage.py ERX1940103/ERX1940103.full-coverage.txt > ERX1940103/ERX1940103.coverage.txt
  rm ERX1940103/ERX1940103.full-coverage.txt
  
  # Mask low coverage regions
  mask-consensus.py \
      ERX1940103 \
      chr1 \
      ERX1940103/ERX1940103.consensus.subs.fa \
      ERX1940103/ERX1940103.subs.vcf \
      ERX1940103/ERX1940103.coverage.txt \
      --mincov 4 > ERX1940103/ERX1940103.consensus.subs.masked.fa
  
  # Clean Up
  rm -rf tmp_snippy/ ERX1940103/reference ERX1940103/ref.fa* ERX1940103/ERX1940103.vcf.gz* chr1.gb
  
  if [[ false == "true" ]]; then
      rm ERX1940103/ERX1940103.bam ERX1940103/ERX1940103.bam.bai
  fi
  
  if [[ false == "false" ]]; then
      find ERX1940103/ -type f |             grep -v -E "\.bam$|\.bai$|\.log$|\.txt$|\.html$|\.tab$" |             xargs -I {} pigz -n --best -p 36 {}
      pigz -n --best -p 36 ERX1940103/ERX1940103.coverage.txt
  fi
  mv ERX1940103/ results/
  mv results/*.log ./
  
  cat <<-END_VERSIONS > versions.yml
  "BACTOPIATOOLS:SNIPPY:SNIPPY_RUN_MODULE":
      bedtools: $(echo $(bedtools --version 2>&1) | sed 's/bedtools v//')
      pigz: $(echo $(pigz --version 2>&1) | sed 's/pigz //')
      snippy: $(echo $(snippy --version 2>&1) | sed 's/^.*snippy //')
      vcf-annotator: $(echo $(vcf-annotator --version 2>&1) | sed 's/vcf-annotator.py //')
  END_VERSIONS

Command exit status:
  1

Command output:
  LOCUS       NZ_LT907989          2961182 bp    DNA     linear   CON 11-FEB-2025

Command error:
  
         total no. multiallelic normalized        : 0
  
         total no. variants normalized            : 13
         total no. variants observed              : 226
         total no. reference observed             : 0
  
  Time elapsed: 0.01s
  
  [13:31:52] Running: snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -c reference/snpeff.config -dataDir . ref ERX1940103.filt.vcf > ERX1940103.vcf 2>> ERX1940103.log
  [13:31:53] Running: /home/nahmed/.bactopia/conda/bioconda--bactopia-variants-1.0.2/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf ERX1940103.vcf > ERX1940103.tab 2>> ERX1940103.log
  [13:31:54] Running: /home/nahmed/.bactopia/conda/bioconda--bactopia-variants-1.0.2/bin/snippy-vcf_extract_subs ERX1940103.filt.vcf > ERX1940103.subs.vcf 2>> ERX1940103.log
  [13:31:54] Running: bcftools convert -Oz -o ERX1940103.vcf.gz ERX1940103.vcf 2>> ERX1940103.log
  [13:31:54] Running: bcftools index -f ERX1940103.vcf.gz 2>> ERX1940103.log
  [13:31:54] Running: bcftools consensus --sample ERX1940103 -f reference/ref.fa -o ERX1940103.consensus.fa ERX1940103.vcf.gz 2>> ERX1940103.log
  [13:31:54] Running: bcftools convert -Oz -o ERX1940103.subs.vcf.gz ERX1940103.subs.vcf 2>> ERX1940103.log
  [13:31:54] Running: bcftools index -f ERX1940103.subs.vcf.gz 2>> ERX1940103.log
  [13:31:54] Running: bcftools consensus --sample ERX1940103 -f reference/ref.fa -o ERX1940103.consensus.subs.fa ERX1940103.subs.vcf.gz 2>> ERX1940103.log
  [13:31:55] Running: rm -f ERX1940103.subs.vcf.gz ERX1940103.subs.vcf.gz.csi ERX1940103.subs.vcf.gz.tbi 2>> ERX1940103.log
  [13:31:55] Generating reference aligned/masked FASTA relative to reference: ERX1940103.aligned.fa
  [13:31:57] Marked 428 heterozygous sites with 'n'
  [13:31:57] Creating extra output files: BED GFF CSV TXT HTML
  [13:31:57] Identified 226 variants.
  [13:31:57] Result folder: ERX1940103
  [13:31:57] Result files:
  [13:31:57] * ERX1940103/ERX1940103.aligned.fa
  [13:31:57] * ERX1940103/ERX1940103.bam
  [13:31:57] * ERX1940103/ERX1940103.bam.bai
  [13:31:57] * ERX1940103/ERX1940103.bed
  [13:31:57] * ERX1940103/ERX1940103.consensus.fa
  [13:31:57] * ERX1940103/ERX1940103.consensus.subs.fa
  [13:31:57] * ERX1940103/ERX1940103.csv
  [13:31:57] * ERX1940103/ERX1940103.filt.vcf
  [13:31:57] * ERX1940103/ERX1940103.gff
  [13:31:57] * ERX1940103/ERX1940103.html
  [13:31:57] * ERX1940103/ERX1940103.log
  [13:31:57] * ERX1940103/ERX1940103.raw.vcf
  [13:31:57] * ERX1940103/ERX1940103.subs.vcf
  [13:31:57] * ERX1940103/ERX1940103.tab
  [13:31:57] * ERX1940103/ERX1940103.txt
  [13:31:57] * ERX1940103/ERX1940103.vcf
  [13:31:57] * ERX1940103/ERX1940103.vcf.gz
  [13:31:57] * ERX1940103/ERX1940103.vcf.gz.csi
  [13:31:57] Walltime used: 51 seconds
  [13:31:57] May the SNPs be with you.
  [13:31:57] Done.
  Traceback (most recent call last):
    File "/home/nahmed/.bactopia/conda/bioconda--bactopia-variants-1.0.2/bin/vcf-annotator", line 20, in <module>
      from Bio import SeqIO
  ModuleNotFoundError: No module named 'Bio'

Work dir:
  /home/nahmed/tsinfer/bactopia/work/c0/e4f57b2b25a583d951e27b393f4b2c

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

    Bactopia Tools Execution Summary
    ------------------------------------
    Workflow         : snippy
    Bactopia Version : 3.2.0
    Nextflow Version : 23.10.1
    Command Line     : nextflow run /home/nahmed/miniconda3/envs/bactopia//share/bactopia-3.2.0/main.nf -w /home/nahmed/tsinfer/bactopia/work/ --wf snippy --mapqual 60 --basequal 13 --mincov 4 --minfrac .75 --bactopia results --reference chr1.gb --max_cpus 36 --max_time 240h --min_time 15000 --nfconfig config.nf --skip_recombination
    Profile          : standard
    Resumed          : false
    Completed At     : 2025-04-15T13:31:57.863483380-07:00
    Duration         : 1h 15m 46s
    Success          : false
    Exit Code        : 1
    Error Report     : Error executing process > 'BACTOPIATOOLS:SNIPPY:SNIPPY_RUN_MODULE (ERX1940103 - chr1)'

Caused by:
  Process `BACTOPIATOOLS:SNIPPY:SNIPPY_RUN_MODULE (ERX1940103 - chr1)` terminated with an error exit status (1)

Command executed:

  if [ "false" == "true" ]; then
      gzip -c -d chr1.gb > chr1.gb
  fi
  
  if ! head -n 1 chr1.gb | grep "^LOCUS"; then
      echo "ERROR: Reference file (chr1.gb) does not appear to be a GenBank file"
      exit 1
  fi
  
  mkdir tmp_snippy/
  snippy \
      --mapqual 60 --basequal 13 --mincov 4 --minfrac .75 --minqual 100 --maxsoft 10 \
      --cpus 36 \
      --outdir ERX1940103 \
      --reference chr1.gb \
      --prefix ERX1940103 \
      --tmpdir tmp_snippy/ \
      --R1 ERX1940103_R1.fastq.gz --R2 ERX1940103_R2.fastq.gz
  
  # Add GenBank annotations
  vcf-annotator ERX1940103/ERX1940103.vcf chr1.gb > ERX1940103/ERX1940103.annotated.vcf
  
  # Get per-base coverage
  grep "^##contig" ERX1940103/ERX1940103.vcf > ERX1940103/ERX1940103.full-coverage.txt
  genomeCoverageBed -ibam ERX1940103/ERX1940103.bam -d >> ERX1940103/ERX1940103.full-coverage.txt
  cleanup-coverage.py ERX1940103/ERX1940103.full-coverage.txt > ERX1940103/ERX1940103.coverage.txt
  rm ERX1940103/ERX1940103.full-coverage.txt
  
  # Mask low coverage regions
  mask-consensus.py \
      ERX1940103 \
      chr1 \
      ERX1940103/ERX1940103.consensus.subs.fa \
      ERX1940103/ERX1940103.subs.vcf \
      ERX1940103/ERX1940103.coverage.txt \
      --mincov 4 > ERX1940103/ERX1940103.consensus.subs.masked.fa
  
  # Clean Up
  rm -rf tmp_snippy/ ERX1940103/reference ERX1940103/ref.fa* ERX1940103/ERX1940103.vcf.gz* chr1.gb
  
  if [[ false == "true" ]]; then
      rm ERX1940103/ERX1940103.bam ERX1940103/ERX1940103.bam.bai
  fi
  
  if [[ false == "false" ]]; then
      find ERX1940103/ -type f |             grep -v -E "\.bam$|\.bai$|\.log$|\.txt$|\.html$|\.tab$" |             xargs -I {} pigz -n --best -p 36 {}
      pigz -n --best -p 36 ERX1940103/ERX1940103.coverage.txt
  fi
  mv ERX1940103/ results/
  mv results/*.log ./
  
  cat <<-END_VERSIONS > versions.yml
  "BACTOPIATOOLS:SNIPPY:SNIPPY_RUN_MODULE":
      bedtools: $(echo $(bedtools --version 2>&1) | sed 's/bedtools v//')
      pigz: $(echo $(pigz --version 2>&1) | sed 's/pigz //')
      snippy: $(echo $(snippy --version 2>&1) | sed 's/^.*snippy //')
      vcf-annotator: $(echo $(vcf-annotator --version 2>&1) | sed 's/vcf-annotator.py //')
  END_VERSIONS

Command exit status:
  1

Command output:
  LOCUS       NZ_LT907989          2961182 bp    DNA     linear   CON 11-FEB-2025

Command error:
  
         total no. multiallelic normalized        : 0
  
         total no. variants normalized            : 13
         total no. variants observed              : 226
         total no. reference observed             : 0
  
  Time elapsed: 0.01s
  
  [13:31:52] Running: snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -c reference/snpeff.config -dataDir . ref ERX1940103.filt.vcf > ERX1940103.vcf 2>> ERX1940103.log
  [13:31:53] Running: /home/nahmed/.bactopia/conda/bioconda--bactopia-variants-1.0.2/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf ERX1940103.vcf > ERX1940103.tab 2>> ERX1940103.log
  [13:31:54] Running: /home/nahmed/.bactopia/conda/bioconda--bactopia-variants-1.0.2/bin/snippy-vcf_extract_subs ERX1940103.filt.vcf > ERX1940103.subs.vcf 2>> ERX1940103.log
  [13:31:54] Running: bcftools convert -Oz -o ERX1940103.vcf.gz ERX1940103.vcf 2>> ERX1940103.log
  [13:31:54] Running: bcftools index -f ERX1940103.vcf.gz 2>> ERX1940103.log
  [13:31:54] Running: bcftools consensus --sample ERX1940103 -f reference/ref.fa -o ERX1940103.consensus.fa ERX1940103.vcf.gz 2>> ERX1940103.log
  [13:31:54] Running: bcftools convert -Oz -o ERX1940103.subs.vcf.gz ERX1940103.subs.vcf 2>> ERX1940103.log
  [13:31:54] Running: bcftools index -f ERX1940103.subs.vcf.gz 2>> ERX1940103.log
  [13:31:54] Running: bcftools consensus --sample ERX1940103 -f reference/ref.fa -o ERX1940103.consensus.subs.fa ERX1940103.subs.vcf.gz 2>> ERX1940103.log
  [13:31:55] Running: rm -f ERX1940103.subs.vcf.gz ERX1940103.subs.vcf.gz.csi ERX1940103.subs.vcf.gz.tbi 2>> ERX1940103.log
  [13:31:55] Generating reference aligned/masked FASTA relative to reference: ERX1940103.aligned.fa
  [13:31:57] Marked 428 heterozygous sites with 'n'
  [13:31:57] Creating extra output files: BED GFF CSV TXT HTML
  [13:31:57] Identified 226 variants.
  [13:31:57] Result folder: ERX1940103
  [13:31:57] Result files:
  [13:31:57] * ERX1940103/ERX1940103.aligned.fa
  [13:31:57] * ERX1940103/ERX1940103.bam
  [13:31:57] * ERX1940103/ERX1940103.bam.bai
  [13:31:57] * ERX1940103/ERX1940103.bed
  [13:31:57] * ERX1940103/ERX1940103.consensus.fa
  [13:31:57] * ERX1940103/ERX1940103.consensus.subs.fa
  [13:31:57] * ERX1940103/ERX1940103.csv
  [13:31:57] * ERX1940103/ERX1940103.filt.vcf
  [13:31:57] * ERX1940103/ERX1940103.gff
  [13:31:57] * ERX1940103/ERX1940103.html
  [13:31:57] * ERX1940103/ERX1940103.log
  [13:31:57] * ERX1940103/ERX1940103.raw.vcf
  [13:31:57] * ERX1940103/ERX1940103.subs.vcf
  [13:31:57] * ERX1940103/ERX1940103.tab
  [13:31:57] * ERX1940103/ERX1940103.txt
  [13:31:57] * ERX1940103/ERX1940103.vcf
  [13:31:57] * ERX1940103/ERX1940103.vcf.gz
  [13:31:57] * ERX1940103/ERX1940103.vcf.gz.csi
  [13:31:57] Walltime used: 51 seconds
  [13:31:57] May the SNPs be with you.
  [13:31:57] Done.
  Traceback (most recent call last):
    File "/home/nahmed/.bactopia/conda/bioconda--bactopia-variants-1.0.2/bin/vcf-annotator", line 20, in <module>
      from Bio import SeqIO
  ModuleNotFoundError: No module named 'Bio'

Work dir:
  /home/nahmed/tsinfer/bactopia/work/c0/e4f57b2b25a583d951e27b393f4b2c

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
    Launch Dir       : /home/nahmed/tsinfer/bactopia
    Merged Results   : results/bactopia-runs/snippy-20250415-121610
    
WARN: Killing running tasks (1)

executor >  local (89)
[98/3a8e82] process > BACTOPIATOOLS:SNIPPY:SNIPPY... [ 76%] 88 of 115, failed...
[-        ] process > BACTOPIATOOLS:SNIPPY:SNIPPY... -
[-        ] process > BACTOPIATOOLS:SNIPPY:SNPDIS... -
[-        ] process > BACTOPIATOOLS:SNIPPY:IQTREE... -
[-        ] process > BACTOPIATOOLS:CUSTOM_DUMPSO... -
ERROR ~ Error executing process > 'BACTOPIATOOLS:SNIPPY:SNIPPY_RUN_MODULE (ERX1940103 - chr1)'

Caused by:
  Process `BACTOPIATOOLS:SNIPPY:SNIPPY_RUN_MODULE (ERX1940103 - chr1)` terminated with an error exit status (1)

Command executed:

  if [ "false" == "true" ]; then
      gzip -c -d chr1.gb > chr1.gb
  fi
  
  if ! head -n 1 chr1.gb | grep "^LOCUS"; then
      echo "ERROR: Reference file (chr1.gb) does not appear to be a GenBank file"
      exit 1
  fi
  
  mkdir tmp_snippy/
  snippy \
      --mapqual 60 --basequal 13 --mincov 4 --minfrac .75 --minqual 100 --maxsoft 10 \
      --cpus 36 \
      --outdir ERX1940103 \
      --reference chr1.gb \
      --prefix ERX1940103 \
      --tmpdir tmp_snippy/ \
      --R1 ERX1940103_R1.fastq.gz --R2 ERX1940103_R2.fastq.gz
  
  # Add GenBank annotations
  vcf-annotator ERX1940103/ERX1940103.vcf chr1.gb > ERX1940103/ERX1940103.annotated.vcf
  
  # Get per-base coverage
  grep "^##contig" ERX1940103/ERX1940103.vcf > ERX1940103/ERX1940103.full-coverage.txt
  genomeCoverageBed -ibam ERX1940103/ERX1940103.bam -d >> ERX1940103/ERX1940103.full-coverage.txt
  cleanup-coverage.py ERX1940103/ERX1940103.full-coverage.txt > ERX1940103/ERX1940103.coverage.txt
  rm ERX1940103/ERX1940103.full-coverage.txt
  
  # Mask low coverage regions
  mask-consensus.py \
      ERX1940103 \
      chr1 \
      ERX1940103/ERX1940103.consensus.subs.fa \
      ERX1940103/ERX1940103.subs.vcf \
      ERX1940103/ERX1940103.coverage.txt \
      --mincov 4 > ERX1940103/ERX1940103.consensus.subs.masked.fa
  
  # Clean Up
  rm -rf tmp_snippy/ ERX1940103/reference ERX1940103/ref.fa* ERX1940103/ERX1940103.vcf.gz* chr1.gb
  
  if [[ false == "true" ]]; then
      rm ERX1940103/ERX1940103.bam ERX1940103/ERX1940103.bam.bai
  fi
  
  if [[ false == "false" ]]; then
      find ERX1940103/ -type f |             grep -v -E "\.bam$|\.bai$|\.log$|\.txt$|\.html$|\.tab$" |             xargs -I {} pigz -n --best -p 36 {}
      pigz -n --best -p 36 ERX1940103/ERX1940103.coverage.txt
  fi
  mv ERX1940103/ results/
  mv results/*.log ./
  
  cat <<-END_VERSIONS > versions.yml
  "BACTOPIATOOLS:SNIPPY:SNIPPY_RUN_MODULE":
      bedtools: $(echo $(bedtools --version 2>&1) | sed 's/bedtools v//')
      pigz: $(echo $(pigz --version 2>&1) | sed 's/pigz //')
      snippy: $(echo $(snippy --version 2>&1) | sed 's/^.*snippy //')
      vcf-annotator: $(echo $(vcf-annotator --version 2>&1) | sed 's/vcf-annotator.py //')
  END_VERSIONS

Command exit status:
  1

Command output:
  LOCUS       NZ_LT907989          2961182 bp    DNA     linear   CON 11-FEB-2025

Command error:
  
         total no. multiallelic normalized        : 0
  
         total no. variants normalized            : 13
         total no. variants observed              : 226
         total no. reference observed             : 0
  
  Time elapsed: 0.01s
  
  [13:31:52] Running: snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -c reference/snpeff.config -dataDir . ref ERX1940103.filt.vcf > ERX1940103.vcf 2>> ERX1940103.log
  [13:31:53] Running: /home/nahmed/.bactopia/conda/bioconda--bactopia-variants-1.0.2/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf ERX1940103.vcf > ERX1940103.tab 2>> ERX1940103.log
  [13:31:54] Running: /home/nahmed/.bactopia/conda/bioconda--bactopia-variants-1.0.2/bin/snippy-vcf_extract_subs ERX1940103.filt.vcf > ERX1940103.subs.vcf 2>> ERX1940103.log
  [13:31:54] Running: bcftools convert -Oz -o ERX1940103.vcf.gz ERX1940103.vcf 2>> ERX1940103.log
  [13:31:54] Running: bcftools index -f ERX1940103.vcf.gz 2>> ERX1940103.log
  [13:31:54] Running: bcftools consensus --sample ERX1940103 -f reference/ref.fa -o ERX1940103.consensus.fa ERX1940103.vcf.gz 2>> ERX1940103.log
  [13:31:54] Running: bcftools convert -Oz -o ERX1940103.subs.vcf.gz ERX1940103.subs.vcf 2>> ERX1940103.log
  [13:31:54] Running: bcftools index -f ERX1940103.subs.vcf.gz 2>> ERX1940103.log
  [13:31:54] Running: bcftools consensus --sample ERX1940103 -f reference/ref.fa -o ERX1940103.consensus.subs.fa ERX1940103.subs.vcf.gz 2>> ERX1940103.log
  [13:31:55] Running: rm -f ERX1940103.subs.vcf.gz ERX1940103.subs.vcf.gz.csi ERX1940103.subs.vcf.gz.tbi 2>> ERX1940103.log
  [13:31:55] Generating reference aligned/masked FASTA relative to reference: ERX1940103.aligned.fa
  [13:31:57] Marked 428 heterozygous sites with 'n'
  [13:31:57] Creating extra output files: BED GFF CSV TXT HTML
  [13:31:57] Identified 226 variants.
  [13:31:57] Result folder: ERX1940103
  [13:31:57] Result files:
  [13:31:57] * ERX1940103/ERX1940103.aligned.fa
  [13:31:57] * ERX1940103/ERX1940103.bam
  [13:31:57] * ERX1940103/ERX1940103.bam.bai
  [13:31:57] * ERX1940103/ERX1940103.bed
  [13:31:57] * ERX1940103/ERX1940103.consensus.fa
  [13:31:57] * ERX1940103/ERX1940103.consensus.subs.fa
  [13:31:57] * ERX1940103/ERX1940103.csv
  [13:31:57] * ERX1940103/ERX1940103.filt.vcf
  [13:31:57] * ERX1940103/ERX1940103.gff
  [13:31:57] * ERX1940103/ERX1940103.html
  [13:31:57] * ERX1940103/ERX1940103.log
  [13:31:57] * ERX1940103/ERX1940103.raw.vcf
  [13:31:57] * ERX1940103/ERX1940103.subs.vcf
  [13:31:57] * ERX1940103/ERX1940103.tab
  [13:31:57] * ERX1940103/ERX1940103.txt
  [13:31:57] * ERX1940103/ERX1940103.vcf
  [13:31:57] * ERX1940103/ERX1940103.vcf.gz
  [13:31:57] * ERX1940103/ERX1940103.vcf.gz.csi
  [13:31:57] Walltime used: 51 seconds
  [13:31:57] May the SNPs be with you.
  [13:31:57] Done.
  Traceback (most recent call last):
    File "/home/nahmed/.bactopia/conda/bioconda--bactopia-variants-1.0.2/bin/vcf-annotator", line 20, in <module>
      from Bio import SeqIO
  ModuleNotFoundError: No module named 'Bio'

Work dir:
  /home/nahmed/tsinfer/bactopia/work/c0/e4f57b2b25a583d951e27b393f4b2c

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

Is this because half of the sequence has nothing to align to? Is this the correct way one would align to chr1?

Thanks so much for your help!

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