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ReSeq simulation errors out when run on Singularity #23

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aperz opened this issue Mar 21, 2024 · 0 comments
Open

ReSeq simulation errors out when run on Singularity #23

aperz opened this issue Mar 21, 2024 · 0 comments

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@aperz
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aperz commented Mar 21, 2024

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                               │
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