reseq seqToIllumina hangs indefinitely after 10000 reads

[ajw2329]

Hello -- thanks for the great tool!

I've been trying to use seqToIllumina but am consistently running into an issue where reseq hangs after generating 10000 reads and must be manually cancelled. The output fastq for those first 10000 reads looks normal save that the last read is truncated.

Here's the command I'm using:

reseq seqToIllumina \
    -j 12 \
    -i test_input.fa \
    -o test_output.fq \
    -s Hs-Nova-TruSeq.reseq

Where the profile Hs-Nova-TruSeq.reseqwas downloaded from your [ReSeq-profiles repo](https://github.com/schmeing/ReSeq-profiles, a few times in case corruption of that file was the issue.

My terminal output looks normal but then hangs after the following:

>>> 03-04-24 15:16:55: info:  Randomly generated seed is 1955184702
>>> 03-04-24 15:16:55: info:  Starting read generation
>>> 03-04-24 15:16:56: info:  Generated 10000 reads.

This happens using both the conda package and when I've manually compiled reseq, and it seems to happen both on a CentOS 7 cluster, and also on a Red Hat Enterprise 8.6 cluster. I've given the jobs lots of RAM (up to 100G).

I've attached an example input fasta (though it happens with all fastas I've tried with >= 10000 reads) and output (truncated) fastq.

Any help here would be very much appreciated -- thanks!!

test_input.fa.zip test_output.fq.zip

[JYLeeBioinfo]

Exactly same issue here, with bioconda build...

I have just settled with running multiple times up to the number of reads intended.