I am encountering an issue while running pbrun fq2bamfast
using NVIDIA Clara Parabricks version 4.3.0-1. The error message I receive is: “Workspace not big enough, expected desiredSize <= cubWorkspaceSize.”
I executed the following commands in a Docker container:
docker run --gpus "device=0" -it --volume /home/user_home/ylf/data:/input_data nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1 /bin/bash
pbrun fq2bamfast --bwa-cpu-thread-pool 16 --ref GRCh38.d1.vd1.fa --in-fq SRR7890824.trimmo_1P SRR7890824.trimmo_2P --out-bam clara_SRR78924.bam --gpusort --gpuwrite --tmp-dir /input_data
Here are the details of my environment:
- Server: Local single-node server
- Memory: 500 GB
- GPUs: 4x RTX A6000, each with 48 GB of VRAM
- CPUs: 2x Intel(R) Xeon(R) Platinum 8373 (144 threads in total)
- Storage (relevant partitions):
(base) [ylf@a6000 ~]$ df -lh Filesystem Size Used Avail Use% Mounted on devtmpfs 252G 0 252G 0% /dev tmpfs 252G 0 252G 0% /dev/shm tmpfs 252G 20M 252G 1% /run
tmpfs 252G 0 252G 0% /sys/fs/cgroup
/dev/mapper/rl-root 70G 54G 17G 78% /
/dev/mapper/rl-home 856G 68G 789G 8% /home
/dev/nvme0n1p2 1014M 888M 127M 88% /boot
/dev/nvme0n1p1 599M 5.8M 594M 1% /boot/efi
/dev/sda 22T 2.9T 18T 14% /home/user_home
tmpfs 51G 24K 51G 1% /run/user/42
tmpfs 51G 4.0K 51G 1% /run/user/1014
The fastq files, SRR7890824.trimmo_1P
and SRR7890824.trimmo_2P
, are each approximately 205 GB in size.
run log:
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /input_data/SRR7890824.trimmo_1P and /input_data/SRR7890824.trimmo_2P
[Parabricks Options Mesg]: @RG\tID:SRR7890824.1.1\tLB:lib1\tPL:bar\tSM:sample\tPU:SRR7890824.1.1
[PB Info 2024-Mar-28 10:41:30] ------------------------------------------------------------------------------
[PB Info 2024-Mar-28 10:41:30] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Mar-28 10:41:30] || Version 4.3.0-1 ||
[PB Info 2024-Mar-28 10:41:30] || GPU-PBBWA mem, Sorting Phase-I ||
[PB Info 2024-Mar-28 10:41:30] ------------------------------------------------------------------------------
[PB Info 2024-Mar-28 10:41:30] Mode = pair-ended-gpu
[PB Info 2024-Mar-28 10:41:30] Running with 4 GPU(s), using 4 stream(s) per device with 16 worker threads per GPU
[PB Info 2024-Mar-28 10:41:40] # 0 0 0 0 0 0 pool: 0 0 bases/GPU/minute: 0.0
[PB Info 2024-Mar-28 10:41:50] # 16 0 3 0 0 0 pool: 15 1435561660 bases/GPU/minute: 2153342490.0
[PB Info 2024-Mar-28 10:42:00] # 7 0 5 0 0 0 pool: 23 3303803447 bases/GPU/minute: 2802362680.5
[PB Info 2024-Mar-28 10:42:10] # 26 0 6 0 0 0 pool: 10 5191614439 bases/GPU/minute: 2831716488.0
[PB Info 2024-Mar-28 10:42:20] # 18 0 6 0 0 0 pool: 18 7059782437 bases/GPU/minute: 2802251997.0
......
[PB Info 2024-Mar-28 10:50:50] # 5 0 4 0 0 0 pool: 43 50432955844 bases/GPU/minute: 1505101711.5
[PB Info 2024-Mar-28 10:51:00] # 0 0 0 0 0 0 pool: 71 51318219378 bases/GPU/minute: 1327895301.0
[PB Info 2024-Mar-28 10:51:10] # 2 0 6 0 0 0 pool: 45 51928108455 bases/GPU/minute: 914833615.5
[PB Info 2024-Mar-28 10:51:20] # 0 0 0 0 0 0 pool: 71 52823192686 bases/GPU/minute: 1342626346.5
[PB Info 2024-Mar-28 10:51:30] # 14 0 0 0 0 0 pool: 41 54023253713 bases/GPU/minute: 1800091540.5
[PB Info 2024-Mar-28 10:51:40] # 0 0 0 0 0 0 pool: 71 54918316026 bases/GPU/minute: 1342593469.5
[PB Info 2024-Mar-28 10:51:50] # 0 0 0 0 0 0 pool: 70 55478973487 bases/GPU/minute: 840986191.5
[PB Info 2024-Mar-28 10:52:00] # 4 0 3 1 0 0 pool: 43 55823232626 bases/GPU/minute: 516388708.5
[PB Info 2024-Mar-28 10:52:10] # 0 0 0 0 0 0 pool: 71 56423277992 bases/GPU/minute: 900068049.0
[PB Info 2024-Mar-28 10:52:20] # 34 0 6 0 0 0 pool: 11 57308539298 bases/GPU/minute: 1327891959.0
[PB Info 2024-Mar-28 10:52:30] # 0 0 0 0 0 0 pool: 71 58223339419 bases/GPU/minute: 1372200181.5
[PB Info 2024-Mar-28 10:52:40] # 0 0 0 0 0 0 pool: 71 58823383734 bases/GPU/minute: 900066472.5
[PB Info 2024-Mar-28 10:52:50] # 0 0 0 0 0 0 pool: 71 59423497320 bases/GPU/minute: 900170379.0
[PB Info 2024-Mar-28 10:53:00] # 5 0 4 0 0 0 pool: 43 60328704814 bases/GPU/minute: 1357811241.0
[PB Info 2024-Mar-28 10:53:10] # 0 0 0 0 0 0 pool: 71 61223873594 bases/GPU/minute: 1342753170.0
[PB Info 2024-Mar-28 10:53:20] # 0 0 0 0 0 0 pool: 69 62089491874 bases/GPU/minute: 1298427420.0
[PB Error 2024-Mar-28 10:53:26][src/internal/pb_fmindex.cu:1336] Workspace not big enough, expected desiredSize <= cubWorkspaceSize, exiting.
For technical support visit https://docs.nvidia.com/clara/index.html#parabricks
Exiting...
Could not run fq2bamfast
Exiting pbrun ...
Thank you in advance for your assistance!