ReSeq
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Published
20 hours ago •
schmeing
schmeing
ReSeq simulation errors out when run on Singularity
Running ReSeq on a Singularity container. I tried some of the container image versions from this image repository, all are giving the same error.
It runs fine without the simulation part (using the --stopAfterEstimation fIag).
Data I'm using:
genome.fasta
test.paired_end.sorted.bam
Any idea why the simulation part might be causing this error?
│ Command executed: │
│ │
│ reseq illuminaPE \ │
│ -c 1 --seed 11111 --adapterFile TruSeq_single \ │
│ -j 2 \ │
│ -r genome.fasta \ │
│ -b test.paired_end.sorted.bam \ │
│ -1 test_bam.1.fastq.gz \ │
│ -2 test_bam.2.fastq.gz │
│ │
│ cat <<-END_VERSIONS > versions.yml │
│ "RESEQ": │
│ reseq: $(reseq --version |& sed 's/ReSeq version //g') │
│ END_VERSIONS │
│ │
│ Command exit status: │
│ 134 │
│ │
│ Command output: │
│ (empty) │
│ │
│ Command error: │
│ >>> 21-03-24 15:01:47: info: Running ReSeq version 1.1 in illuminaPE mode │
│ >>> 21-03-24 15:01:47: info: Reading reference from genome.fasta │
│ >>> 21-03-24 15:01:47: info: Read in 1 reference sequences. │
│ >>> 21-03-24 15:01:47: info: Reading mapping from test.paired_end.sorted.bam │
│ >>> 21-03-24 15:01:47: info: Storing real data statistics in test.paired_end.sorted.bam.reseq │
│ terminate called after throwing an instance of 'std::logic_error' │
│ what(): basic_string: construction from null is not valid │
│ .command.sh: line 8: 40 Aborted (core dumped) reseq illuminaPE -c 1 --seed 11111 --adapterFile TruSeq_single -j 2 -r genome.fasta -b test.paired_end.sorted.bam -1 test_bam.1.fastq.gz -2 test_bam.2.fastq.gz │
