Error with minimap2 with Parabrick v4.3

Healthcare & Life Sciences Parabricks
1

Hi,

I’m trying to use pbrun minimap2 on ONT data. However I keep getting an error. I’m using Parabricks v4.3. See command and output below. Any advise? Thanks

apptainer exec --nv /data/singularity-containers/clara-parabricks_4.3.0-1.sif pbrun minimap2 \
    --ref /data/references/GRCh38.primary_assembly.genome.fa \
    --preset map-ont \
    --num-threads 35 \
    --low-memory \
    --out-bam /data/out.bam \
    --in-fq /data/all_pass.vhg002v1.fastq

[PB Info 2024-Mar-21 15:51:54] ------------------------------------------------------------------------------
[PB Info 2024-Mar-21 15:51:54] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Mar-21 15:51:54] || Version 4.3.0-1 ||
[PB Info 2024-Mar-21 15:51:54] || minimap2 ||
[PB Info 2024-Mar-21 15:51:54] ------------------------------------------------------------------------------
[PB Info 2024-Mar-21 15:51:54] Reading reference file.
[PB Info 2024-Mar-21 15:53:19] -------------------------------------
[PB Info 2024-Mar-21 15:53:19] Elapsed-Minutes Processed-Reads
[PB Info 2024-Mar-21 15:53:19] -------------------------------------
[PB Info 2024-Mar-21 15:53:19] 0.0 0
[PB Info 2024-Mar-21 15:53:25] 0.1 0
[PB Info 2024-Mar-21 15:53:31] 0.2 0
[PB Info 2024-Mar-21 15:53:38] 0.3 0
[PB Info 2024-Mar-21 15:53:44] 0.4 0
[PB Info 2024-Mar-21 15:53:50] 0.5 0
[PB Info 2024-Mar-21 15:53:56] 0.6 0
[PB Info 2024-Mar-21 15:54:02] 0.7 0
[PB Error 2024-Mar-21 15:54:06][/home/jenkins/agent/workspace/parabricks-branch-build//filehandle/inc/compressfile.h:317] Too much meta-data: 1125504 bytes, max of 1048576, exiting.
For technical support visit NVIDIA Clara - NVIDIA Docs

2

Hi,

Thanks for your posting here! We have confirmed that this is a bug in Parabricks v4.3 and we are working on fixing it. You will get a fixed version in our next release.

2 Likes
3

Hello, v4.3.1 has been released with a fix for the issue you reported. NVIDIA Parabricks | NVIDIA NGC

1 Like
4

Hi, I am running into a similar problem with ONT data with parabrick 4.3.2-1.
I run:
docker run
–gpus all
–rm
–volume $(pwd):/workdir
–volume $(pwd):/outputdir
nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1
pbrun minimap2
–ref /workdir/ref.fa
–in-fq /workdir/fastq/sequences.fastq.gz
–out-bam /outputdir/output.bam
–preset map-ont
–logfile /workdir/logfile.txt

[PB Info 2025-Mar-24 14:18:05] ------------------------------------------------------------------------------
[PB Info 2025-Mar-24 14:18:05] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2025-Mar-24 14:18:05] || Version 4.3.2-1 ||
[PB Info 2025-Mar-24 14:18:05] || minimap2 ||
[PB Info 2025-Mar-24 14:18:05] ------------------------------------------------------------------------------
[PB Info 2025-Mar-24 14:18:06] Reading reference file.
[PB Info 2025-Mar-24 14:18:06] -------------------------------------
[PB Info 2025-Mar-24 14:18:06] Elapsed-Minutes Processed-Reads
[PB Info 2025-Mar-24 14:18:06] -------------------------------------
[PB Info 2025-Mar-24 14:18:06] 0.0 0
[PB Info 2025-Mar-24 14:18:12] 0.1 0
[PB Info 2025-Mar-24 14:18:18] 0.2 0
[PB Info 2025-Mar-24 14:18:24] 0.3 0
[PB Info 2025-Mar-24 14:18:30] 0.4 0
[PB Info 2025-Mar-24 14:18:36] 0.5 0
[PB Info 2025-Mar-24 14:18:42] 0.6 0
[PB Info 2025-Mar-24 14:18:48] 0.7 0
[PB Info 2025-Mar-24 14:18:54] 0.8 0
[PB Info 2025-Mar-24 14:19:00] 0.9 0

It just stays at 0 reads processed for over 10 min. When I also parse a reference.mmi file with
–index /workdir/ref.mmi
I get:
PB Info 2025-Mar-24 14:10:38] ------------------------------------------------------------------------------
[PB Info 2025-Mar-24 14:10:38] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2025-Mar-24 14:10:38] || Version 4.3.2-1 ||
[PB Info 2025-Mar-24 14:10:38] || minimap2 ||
[PB Info 2025-Mar-24 14:10:38] ------------------------------------------------------------------------------
[PB Info 2025-Mar-24 14:10:38] Reading reference file.
[PB Error 2025-Mar-24 14:10:38][minimap2-src/index.c:708] fread returned 0, exiting.
For technical support visit NVIDIA Clara - NVIDIA Docs
Exiting…

Can you give me any advice where the problem might be? Thanks