Fq2bam --align-only flag leads to segmentation fault

Healthcare & Life Sciences Parabricks
1

I was happy to see the --align-only flag in Parabricks fq2bam v4.1, as my pipeline downstream of bwa-mem takes name-sorted bam.

However, in my hands, the --align-only flag leads to a segmentation fault.

WITHOUT THE FLAG

[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /workdir/input/unmerged_1.fastq.gz and
/workdir/input/unmerged_2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:1.1\tLB:lib1\tPL:bar\tSM:sample\tPU:1.1
[PB Info 2023-Jul-13 14:28:45] ------------------------------------------------------------------------------
[PB Info 2023-Jul-13 14:28:45] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2023-Jul-13 14:28:45] ||                              Version 4.1.1-1                             ||
[PB Info 2023-Jul-13 14:28:45] ||                       GPU-BWA mem, Sorting Phase-I                       ||
[PB Info 2023-Jul-13 14:28:45] ------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[PB Info 2023-Jul-13 14:28:50] GPU-BWA mem
etc.

WITH THE FLAG

[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /workdir/input/unmerged_1.fastq.gz and
/workdir/input/unmerged_2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:1.1\tLB:lib1\tPL:bar\tSM:sample\tPU:1.1
[PB Info 2023-Jul-13 14:42:59] ------------------------------------------------------------------------------
[PB Info 2023-Jul-13 14:42:59] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2023-Jul-13 14:42:59] ||                              Version 4.1.1-1                             ||
[PB Info 2023-Jul-13 14:42:59] ||                       GPU-BWA mem, Sorting Phase-I                       ||
[PB Info 2023-Jul-13 14:42:59] ------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[PB Error 2023-Jul-13 14:43:04][-unknown-:0] Received signal: 11
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I am running the clara-parabricks-4.1.1-1 container using singularity on a cluster server running Slurm. The job is on a shared node, using only 1 of several GPUs. This all seems fine, since the job executes properly without --align-only.

The command is:

pbrun fq2bam \
    --logfile output/$LOG_FILE_NAME \
    --out-bam output/$OUT_FILE_NAME \
    --in-fq input/unmerged_1.fastq.gz input/unmerged_2.fastq.gz \
    --fix-mate \
    --ref input/$GENOME_FASTA \
    --bwa-options=-Y \
    --tmp-dir tmp \
    --filter-flag 256 \
    --align-only

This seems like a bug, perhaps one that only appears with a specific combination of options?

Thanks for any help, I’d like to use the new flag.