Issue with nvcr.io/nvidia/clara/clara-parabricks:4.3.1-1 docker

Healthcare & Life Sciences Parabricks
1

When I try to run:
pbrun collectmultiplemetrics --ref Homo_sapiens_assembly19.fasta --bam /path/to/input/bam --out-qc-metrics-dir /path/to/outdir --geo-all-metrics

I get the below errors:

[PB Info 2024-Jun-28 17:05:58] ------------------------------------------------------------------------------
[PB Info 2024-Jun-28 17:05:58] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Jun-28 17:05:58] || Version 4.3.1-1 ||
[PB Info 2024-Jun-28 17:05:58] || collectmultiplemetrics ||
[PB Info 2024-Jun-28 17:05:58] ------------------------------------------------------------------------------
[PB Info 2024-Jun-28 17:05:58] Using 1 GPUs, 3 BAM decompressor threads, 8 GC calculator threads
Chunk size 1000 (# of BAM records/chunk)
Recycle bin size 100 (# of reusable chunks)
Processor SPSC queue size 100 (# of chunks per processor thread)
[PB Info 2024-Jun-28 17:05:58] Loading Reference
Homo_sapiens_assembly19.fasta

[PB Info 2024-Jun-28 17:06:12] Reference loaded
terminate called after throwing an instance of ‘std::system_error’
what(): Operation not permitted
[PB e[31mErrore[0m 2024-Jun-28 17:06:12][-unknown-:0] Received signal: 6

For technical support visit NVIDIA Clara - NVIDIA Docs, exiting.

Exiting…

Please visit NVIDIA Clara - NVIDIA Docs for detailed documentation
Could not run collectmultiplemetrics
Exiting pbrun …

Is this an issue in the docker image? I tried to run fq2bam and I got the same issue. Any help would be much appreciated!

2

Hi @maria_nakhoul,

Is there a typo in your command? --geo-all-metrics should be --gen-all-metrics.

3

yes, it was a typo, it was --gen-all-metrics that gave the above error.