Hello all,
I am facing a problem with the pbrun fq2bam I have two data sets one downloaded from NCBI SRA and one from HGDP (Human genome diversity project). Whenever I am using pbrun on NCBI SRA files it runs smoothly and I get the desired output, however when I am trying the same command with the HGDP files its going into Recovery mode (single end and paired end) and after sometimes it completely shifts to CPU. I am not able to understand why this is happening? I am missing something like I have to do something before passing the data to pbrun.
Any suggestion would be highly appreciated.
(Also the file size from HGDP is around 25gb each and NCBI SRA are around 15 to 17 gb)
I am using a dual GPU system (RTX 4090 24 GB and RTX 5080 16 GB) with 256 GB RAM with 24 Cores.
docker run --gpus all -v /media/eil-lab/DATA4/read_file/:/data nvcr.io/nvidia/clara/clara-parabricks:4.5.1-1 pbrun fq2bam --ref /data/Ref/ref.fasta --in-fq /data/Data/ERR757818_1.fastq.gz /data/Data/ERR757818_2.fastq.gz --out-bam /data/Output/output_1.bam --low-memory --bwa-options=“–reduce-batch-size”
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Set --bwa-options=“-K #” to produce compatible pair-ended results with previous versions of
fq2bam or BWA MEM.
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /data/Data/ERR757818_1.fastq.gz and /data/Data/ERR757818_2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:ERR757818.1.1\tLB:lib1\tPL:bar\tSM:sample\tPU:ERR757818.1.1
[Parabricks Options Mesg]: Using --low-memory sets the number of streams in bwa mem to 1.
[PB Info 2025-Jun-30 04:33:09] ------------------------------------------------------------------------------
[PB Info 2025-Jun-30 04:33:09] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2025-Jun-30 04:33:09] || Version 4.5.1-1 ||
[PB Info 2025-Jun-30 04:33:09] || GPU-PBBWA mem, Sorting Phase-I ||
[PB Info 2025-Jun-30 04:33:09] ------------------------------------------------------------------------------
[PB Info 2025-Jun-30 04:33:09] Mode = pair-ended-gpu
[PB Info 2025-Jun-30 04:33:09] Running with 2 GPU(s), using 1 stream(s) per device with 16 worker threads per GPU
[PB Info 2025-Jun-30 04:33:19] # 0 0 0 0 0 0 pool: 0 0 bases/GPU/minute: 0.0
[PB Info 2025-Jun-30 04:33:29] # 0 0 0 0 0 0 pool: 0 0 bases/GPU/minute: 0.0
[PB Info 2025-Jun-30 04:33:39] # 0 0 0 0 0 0 pool: 0 0 bases/GPU/minute: 0.0
[PB Info 2025-Jun-30 04:33:49] # 17 0 0 0 0 0 pool: 0 0 bases/GPU/minute: 0.0
[PB Info 2025-Jun-30 04:33:59] # 20 8 0 7 0 0 pool: 0 628971049 bases/GPU/minute: 1886913147.0
[PB Info 2025-Jun-30 04:34:09] # 20 0 8 0 0 0 pool: 8 1626730394 bases/GPU/minute: 2993278035.0
[PB Info 2025-Jun-30 04:34:19] # 20 0 8 0 0 0 pool: 8 2651527503 bases/GPU/minute: 3074391327.0
[PB Info 2025-Jun-30 04:34:29] # 20 7 2 7 0 0 pool: 3 3678723323 bases/GPU/minute: 3081587460.0
[PB Info 2025-Jun-30 04:34:36] Single-ended recovery mode for batch with 28033024 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:37] Single-ended recovery mode for batch with 28082176 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28114944 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28131328 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28147712 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28164096 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28180480 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28196864 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28213248 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28229632 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28246016 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28262400 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28278784 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28295168 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:38] Single-ended recovery mode for batch with 28311552 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:39] Single-ended recovery mode for batch with 28327936 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:39] Single-ended recovery mode for batch with 28344320 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:39] Single-ended recovery mode for batch with 28360704 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:39] Single-ended recovery mode for batch with 28377088 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:39] Single-ended recovery mode for batch with 28393472 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:39] Single-ended recovery mode for batch with 28409856 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:39] Single-ended recovery mode for batch with 28426240 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:39] # 19 2 0 10 20 0 pool: 0 4213366463 bases/GPU/minute: 1603929420.0
[PB Info 2025-Jun-30 04:34:39] Single-ended recovery mode for batch with 28442624 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:39] Single-ended recovery mode for batch with 28459008 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:49] # 20 2 0 10 20 0 pool: 0 4213366463 bases/GPU/minute: 0.0
[PB Info 2025-Jun-30 04:34:49] Single-ended recovery mode for batch with 28491776 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:50] Single-ended recovery mode for batch with 28524544 (both ends) reads before itself
[PB Info 2025-Jun-30 04:34:59] # 20 2 0 12 20 0 pool: 0 4218315463 bases/GPU/minute: 14847000.0