ASCIIGenome failing during analysis

[charlesfoster]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/viralrecon pipeline documentation

Description of the bug

While running viralrecon using data from the SNAP/Swift protocol, the pipeline repeatedly crashed at the ASCIIGenome step:

If I skip the ASCIIGenome step (--skip_asciigenome), the pipeline finishes as expected. I was asked to create this issue by @drpatelh (https://nfcore.slack.com/archives/C0110R22NH3/p1623156803141900?thread_ts=1623119196.129800&cid=C0110R22NH3)

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run nf-core/viralrecon --platform illumina --input samplesheet.csv --genome 'NC_045512.2' --protocol amplicon --primer_bed swift.bed --primer_left_suffix '_F' --primer_right_suffix '_R' --ivar_trim_offset 5 --skip_assembly -profile singularity --max_memory "50.0 GB"
2. See error:

Error executing process > 'NFCORE_VIRALRECON:ILLUMINA:VARIANTS_IVAR:ASCIIGENOME (sample1)'

Caused by:
  Process `NFCORE_VIRALRECON:ILLUMINA:VARIANTS_IVAR:ASCIIGENOME (sample1)` terminated with an error exit status (1)

Command executed:

  zcat sample1.vcf.gz \
      | grep -v '#' \
      | awk -v FS='	' -v OFS='	' '{print $1, ($2-50-1), ($2+50)}' \
      > variants.bed
  
  ASCIIGenome \
      -ni \
      -x "trackHeight 0 bam#1 && trackHeight 50 bam@2 && readsAsPairs -on && filterVariantReads && save sample1.%r.pdf" \
      --batchFile variants.bed \
      --fasta GCF_009858895.2_ASM985889v3_genomic.200409.fna \
      sample1.ivar_trim.sorted.bam \
      sample1.vcf.gz \
      swift.bed \
      GCF_009858895.2_ASM985889v3_genomic.200409.gff \
      > /dev/null
  
  echo $(ASCIIGenome -ni --version 2>&1) | sed -e "s/ASCIIGenome //g" > asciigenome.version.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  Cannot read history file '/home/default/.asciigenome.yaml'
  
  Indexing 'GCF_009858895.2_ASM985889v3_genomic.200409.fna'.
  Initializing coordinates... Done from: sample1.ivar_trim.sorted.bam
  Cannot read history file '/home/default/.asciigenome.yaml'
  Invalid coordinates: -36 64
  Exception in thread "main" exceptions.InvalidGenomicCoordsException
  	at tracks.IntervalFeature.validateIntervalFeature(IntervalFeature.java:231)
  	at tracks.IntervalFeature.intervalFeatureFromBedLine(IntervalFeature.java:183)
  	at tracks.IntervalFeature.<init>(IntervalFeature.java:70)
  	at samTextViewer.Main.main(Main.java:150)

Expected behaviour

ASCIIGenome to generate the correct output files, and for the pipeline to complete without error.

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline
• The .nextflow.log file
  nextflow.log

System

• Hardware: Desktop
• Executor: Just a simple nextflow run command
• OS: pop!_os
• Version 20.10

Nextflow Installation

• Version: 21.04.1 build 5556

Container engine

• Engine: Singularity
• version: Unsure
• Image tag: nf-core/viralrecon v2.0

Additional context

What's the best way to privately share some reads that might allow the issue to be replicated?

[drpatelh]

This should be fixed in #202 @charlesfoster. I submitted a PR to create a multi-tool container that contains ASCIIGenome and BEDTools. The interval size adjustment will now be chucked through bedtools slop as an additional step to santise the intervals and to make sure they don't cross chromosomal boundaries. Be great if you can test this when that PR is merged.

nextflow pull nf-core/viralrecon
nextflow run nf-core/viralrecon -r dev <YOUR_PARAMETERS>