container version: clara-parabricks_4.2.0-1
I followed the documentation to run collectmultiplemetrics in singularity but thats generating error due to (probably) missing library: Record contains library that is missing from header
I also noticed a warning:
WARNING: Skipping mount /var/run/nvidia-persistenced/socket [files]: /var/run/nvidia-persistenced/socket doesn’t exist in container
My understanding is the container should be self contained. How to fix this?
singularity_sif=“./clara-parabricks_4.2.0-1.sif”
singularity exec --nv ${singularity_sif} /bin/bash -c “nvidia-smi;
pbrun collectmultiplemetrics
–ref ./Homo_sapiens.GRCh38.110.dna_sm.primary_assembly.fa
–bam ./sample_two_pass_R.bam
–out-qc-metrics-dir ./QC/all-metrics/sample_two_pass_R/
–gen-all-metrics”
[PB Info 2024-Feb-28 06:32:52] ------------------------------------------------------------------------------
[PB Info 2024-Feb-28 06:32:52] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Feb-28 06:32:52] || Version 4.2.0-1 ||
[PB Info 2024-Feb-28 06:32:52] || collectmultiplemetrics ||
[PB Info 2024-Feb-28 06:32:52] ------------------------------------------------------------------------------
[PB Info 2024-Feb-28 06:32:52] Using 4 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-Feb-28 06:32:52] Loading Reference /panfs/accrepfs.vampire/nobackup/h_vmac/user/janveva1/Project/RNAseq/A4/QC/genome_index/Homo_sapiens.GRCh38.110.dna_sm.primary_assembly.fa
[PB Info 2024-Feb-28 06:33:04] Reference loaded
[PB Info 2024-Feb-28 06:33:11] ------------------------------------------------------------------------------
[PB Info 2024-Feb-28 06:33:11] Time-Stamp Elapsed-Minutes Current-Locus
[PB Info 2024-Feb-28 06:33:11] ------------------------------------------------------------------------------
[PB Info 2024-Feb-28 06:33:12] 06:33:12 0.0
[PB Info 2024-Feb-28 06:33:13] 06:33:13 0.0
terminate called after throwing an instance of ‘std::runtime_error’
what(): Record contains library that is missing from header:
[PB ESC[31mErrorESC[0m 2024-Feb-28 06:33:14][-unknown-:0] Received signal: 6
For technical support visit Clara Parabricks v4.2.0 - NVIDIA Docs, exiting.
For technical support visit Clara Parabricks v4.2.0 - NVIDIA Docs
Exiting…
Please visit NVIDIA Clara - NVIDIA Docs for detailed documentation
Could not run collectmultiplemetrics
Exiting pbrun …
detailed log:
WARNING: Skipping mount /var/run/nvidia-persistenced/socket [files]: /var/run/nvidia-persistenced/socket doesn't exist in container
Wed Feb 28 06:32:50 2024
+---------------------------------------------------------------------------------------+
| NVIDIA-SMI 535.129.03 Driver Version: 535.129.03 CUDA Version: 12.2 |
|-----------------------------------------+----------------------+----------------------+
| 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 NVIDIA RTX A6000 Off | 00000000:31:00.0 Off | Off |
| 30% 26C P8 20W / 300W | 3MiB / 49140MiB | 0% Default |
| | | N/A |
+-----------------------------------------+----------------------+----------------------+
| 1 NVIDIA RTX A6000 Off | 00000000:4B:00.0 Off | Off |
| 30% 26C P8 20W / 300W | 3MiB / 49140MiB | 0% Default |
| | | N/A |
+-----------------------------------------+----------------------+----------------------+
| 2 NVIDIA RTX A6000 Off | 00000000:98:00.0 Off | Off |
| 30% 30C P8 31W / 300W | 3MiB / 49140MiB | 0% Default |
| | | N/A |
+-----------------------------------------+----------------------+----------------------+
| 3 NVIDIA RTX A6000 Off | 00000000:CA:00.0 Off | Off |
| 30% 27C P8 20W / 300W | 3MiB / 49140MiB | 0% Default |
| | | N/A |
+-----------------------------------------+----------------------+----------------------+
+---------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=======================================================================================|
| No running processes found |
+---------------------------------------------------------------------------------------+
[PB Info 2024-Feb-28 06:32:52] ------------------------------------------------------------------------------
[PB Info 2024-Feb-28 06:32:52] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Feb-28 06:32:52] || Version 4.2.0-1 ||
[PB Info 2024-Feb-28 06:32:52] || collectmultiplemetrics ||
[PB Info 2024-Feb-28 06:32:52] ------------------------------------------------------------------------------
[PB Info 2024-Feb-28 06:32:52] Using 4 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-Feb-28 06:32:52] Loading Reference /panfs/accrepfs.vampire/nobackup/h_vmac/user/janveva1/Project/RNAseq/A4/QC/genome_index/Homo_sapiens.GRCh38.110.dna_sm.primary_assembly.fa
[PB Info 2024-Feb-28 06:33:04] Reference loaded
[PB Info 2024-Feb-28 06:33:11] ------------------------------------------------------------------------------
[PB Info 2024-Feb-28 06:33:11] Time-Stamp Elapsed-Minutes Current-Locus
[PB Info 2024-Feb-28 06:33:11] ------------------------------------------------------------------------------
[PB Info 2024-Feb-28 06:33:12] 06:33:12 0.0
[PB Info 2024-Feb-28 06:33:13] 06:33:13 0.0
terminate called after throwing an instance of 'std::runtime_error'
what(): Record contains library that is missing from header:
[PB ESC[31mErrorESC[0m 2024-Feb-28 06:33:14][-unknown-:0] Received signal: 6
For technical support visit https://docs.nvidia.com/clara/parabricks/4.2.0/index.html, exiting.
For technical support visit https://docs.nvidia.com/clara/parabricks/4.2.0/index.html
Exiting...
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation
Could not run collectmultiplemetrics
Exiting pbrun ...