Hi Nvidia Team,
I’m receiving an error when trying to run the fq2bam tutorial sample on a Slurm cluster using a singularity container.
#SBATCH --job-name "parabricks_test"
#SBATCH -e /scott/parabricks_test/%x.e%j
#SBATCH -o /scott/parabricks_test/%x.e%j
#SBATCH -N 1 -c 12
#SBATCH --mem 170G
#SBATCH --gpus=1
#SBATCH --tmp=512G
#SBATCH -t 24:00:00
nvidia-smi
module load Singularity/3.7.0
module load python/3.7.6
singularity exec --cleanenv --nv \
-S /localhd/$SLURM_JOBID:/mnt/scratch:512GB \
-B $PWD:/workdir \
-B $PWD:/outputdir \
$singularity_cache/clara-parabricks_4_0_1-1.sif \
pbrun fq2bam \
--ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \
--in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz \
--out-bam /outputdir/fq2bam_output.bam
I see the following output:
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 470.57.02 Driver Version: 470.57.02 CUDA Version: 11.4 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|===============================+======================+======================|
| 0 Tesla V100-PCIE... On | 00000000:00:06.0 Off | 0 |
| N/A 28C P0 24W / 250W | 0MiB / 32510MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| No running processes found |
+-----------------------------------------------------------------------------+
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /workdir/parabricks_sample/Data/sample_1.fq.gz and
/workdir/parabricks_sample/Data/sample_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
[PB Info 2023-Apr-18 00:21:44] ------------------------------------------------------------------------------
[PB Info 2023-Apr-18 00:21:44] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2023-Apr-18 00:21:44] || Version 4.0.1-1 ||
[PB Info 2023-Apr-18 00:21:44] || GPU-BWA mem, Sorting Phase-I ||
[PB Info 2023-Apr-18 00:21:44] ------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[PB Info 2023-Apr-18 00:22:15] GPU-BWA mem
[PB Info 2023-Apr-18 00:22:15] ProgressMeter Reads Base Pairs Aligned
[PB Info 2023-Apr-18 00:23:04] 5043564 580000000
[PB Info 2023-Apr-18 00:23:33] 10087128 1160000000
[PB Info 2023-Apr-18 00:24:03] 15130692 1740000000
[PB Info 2023-Apr-18 00:24:31] 20174256 2320000000
[PB Info 2023-Apr-18 00:24:58] 25217820 2900000000
[PB ESC[31mErrorESC[0m 2023-Apr-18 00:25:10][-unknown-:0] Received signal: 11
For technical support visit https://docs.nvidia.com/clara/parabricks/4.0.0/Help.html, exiting.
For technical support visit https://docs.nvidia.com/clara/parabricks/4.0.0/Help.html
Exiting...
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation
Could not run fq2bam
Exiting pbrun ...
Do you have any insights into what this error is?
Thanks,
Scott