bowtie2 indexes lost for genomes bigger than 4Gbp when --bwt2_index is not provided

[oneillkza]

Check Documentation

I have checked the following places for your error:

• [x ] nf-core website: troubleshooting
• [x ] nf-core/hic pipeline documentation

Description of the bug

When running with the --fasta option (generate indexes on the fly) with a genome larger than 4Gbp, bowtie2 gives the indexes it generates the extension "bt2l" rather than "bt2", and the index doesn't get picked up by subsequent steps, causing the workflow to halt.

See http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#small-and-large-indexes

Steps to reproduce

Steps to reproduce the behaviour:

1. Run with any genome > 4Gbp and without the --bwt2_index option
2. See error:

[Glenn032787]

Here is the error:

Execution cancelled -- Finishing pending tasks before exit
WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException
Error executing process > 'bowtie2_end_to_end (R_R1.7)'

Caused by:
  Process `bowtie2_end_to_end (R_R1.7)` terminated with an error exit status (255)

Command executed:

  INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
    bowtie2 --rg-id BMG --rg SM:R1.7 \
  --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder \
  -p 16 \
  -x ${INDEX} \
  --un R1.7_unmap.fastq \
        -U R1.7.fastq.gz | samtools view -F 4 -bS - > R1.7.bam

Command exit status:
  255

Command output:
  (empty)

Command error:
  (ERR): "--passthrough" does not exist or is not a Bowtie 2 index
  Exiting now ...

The INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//' is not finding bt2l so $INDEX is empty.