The speed of fq2bam_meth doesn’t seem as fast as I expected. Are there any parameters that can be optimized?
my command is :
docker run -it --gpus all -e NVIDIA_DRIVER_CAPABILITIES=all --volume /home/wang_yanni/sc_meth_ATAC/integratioh/fq2bam:/mydata 74f2b983a773 /bin/bash
time pbrun fq2bam_meth --ref hg38.fa --in-se-fq …/deep_board/Airway-S43-2_supplement/A10.1.fastq.gz --out-bam A10_2stream.bam --bwa-nstreams 2 --num-gpus 3 --gpuwrite --bwa-cpu-thread-pool 16
the output is :
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /mydata/deep_board/Airway-S43-2_supplement/A10.R1.fastq.gz
[Parabricks Options Mesg]: @RG\tID:HWYGYDSX7.3\tLB:lib1\tPL:bar\tSM:sample\tPU:HWYGYDSX7.3
[PB Info 2024-Jul-11 16:00:15] ------------------------------------------------------------------------------
[PB Info 2024-Jul-11 16:00:15] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Jul-11 16:00:15] || Version 4.3.1-1 ||
[PB Info 2024-Jul-11 16:00:15] || GPU-PBBWA mem, Sorting Phase-I ||
[PB Info 2024-Jul-11 16:00:15] ------------------------------------------------------------------------------
[PB Info 2024-Jul-11 16:00:15] Mode = single-ended-gpu
[PB Info 2024-Jul-11 16:00:15] Running with 3 GPU(s), using 2 stream(s) per device with 16 worker threads per GPU
[PB Info 2024-Jul-11 16:00:25] # 10 0 0 0 bases/GPU/minute: 0.0
[PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 0 reads before itself
[PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 262144 reads before itself
[PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 65536 reads before itself
[PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 327680 reads before itself
[PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 196608 reads before itself
[PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 393216 reads before itself
[PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 131072 reads before itself
[PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 458752 reads before itself
[PB Info 2024-Jul-11 16:00:30] Time spent reading: 0.655694 seconds
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 524288 reads before itself
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 786432 reads before itself
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 720896 reads before itself
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 851968 reads before itself
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 589824 reads before itself
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 655360 reads before itself
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 917504 reads before itself
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 1179648 reads before itself
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 1048576 reads before itself
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 983040 reads before itself
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 1245184 reads before itself
[PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 1310720 reads before itself
[PB Info 2024-Jul-11 16:00:31] Single-ended recovery mode for batch with 1114112 reads before itself
[PB Info 2024-Jul-11 16:00:35] # 0 1 0 0 bases/GPU/minute: 0.0
[PB Info 2024-Jul-11 16:00:45] # 0 1 0 0 bases/GPU/minute: 0.0
[PB Info 2024-Jul-11 16:00:55] # 0 0 0 30789160 bases/GPU/minute: 61578320.0
[PB Info 2024-Jul-11 16:01:05] # 0 0 0 30789160 bases/GPU/minute: 0.0
[PB Info 2024-Jul-11 16:01:15] # 0 0 0 59753069 bases/GPU/minute: 57927818.0
[PB Info 2024-Jul-11 16:01:25] # 0 0 0 59753069 bases/GPU/minute: 0.0
[PB Info 2024-Jul-11 16:01:35] # 0 0 0 88726172 bases/GPU/minute: 57946206.0
[PB Info 2024-Jul-11 16:01:45] # 0 0 0 88726172 bases/GPU/minute: 0.0
[PB Info 2024-Jul-11 16:01:55] # 0 0 0 117878289 bases/GPU/minute: 58304234.0
[PB Info 2024-Jul-11 16:02:05] # 0 0 0 147031106 bases/GPU/minute: 58305634.0
[PB Info 2024-Jul-11 16:02:15] # 0 0 0 147031106 bases/GPU/minute: 0.0
[PB Info 2024-Jul-11 16:02:25] # 0 0 0 176147936 bases/GPU/minute: 58233660.0
[PB Info 2024-Jul-11 16:02:35] # 0 0 0 176147936 bases/GPU/minute: 0.0
[PB Info 2024-Jul-11 16:02:45] # 0 0 0 205281290 bases/GPU/minute: 58266708.0
[PB Info 2024-Jul-11 16:02:55] Rate stats (based on sampling every 10 seconds):
min rate: 0.0 bases/GPU/minute
max rate: 61578320.0 bases/GPU/minute
avg rate: 27370838.7 bases/GPU/minute
[PB Info 2024-Jul-11 16:02:55] Time spent monitoring (multiple of 10): 160.010
[PB Info 2024-Jul-11 16:02:55] bwalib run finished in 151.575 seconds
[PB Info 2024-Jul-11 16:02:55] ------------------------------------------------------------------------------
[PB Info 2024-Jul-11 16:02:55] || Program: GPU-PBBWA mem, Sorting Phase-I ||
[PB Info 2024-Jul-11 16:02:55] || Version: 4.3.1-1 ||
[PB Info 2024-Jul-11 16:02:55] || Start Time: Thu Jul 11 16:00:15 2024 ||
[PB Info 2024-Jul-11 16:02:55] || End Time: Thu Jul 11 16:02:55 2024 ||
[PB Info 2024-Jul-11 16:02:55] || Total Time: 2 minutes 40 seconds ||
[PB Info 2024-Jul-11 16:02:55] ------------------------------------------------------------------------------
[PB Info 2024-Jul-11 16:02:58] ------------------------------------------------------------------------------
[PB Info 2024-Jul-11 16:02:58] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Jul-11 16:02:58] || Version 4.3.1-1 ||
[PB Info 2024-Jul-11 16:02:58] || Sorting Phase-II ||
[PB Info 2024-Jul-11 16:02:58] ------------------------------------------------------------------------------
[PB Info 2024-Jul-11 16:02:58] progressMeter - Percentage
[PB Info 2024-Jul-11 16:02:58] 0.0
[PB Info 2024-Jul-11 16:03:03] Sorting and Marking: 5.001 seconds
[PB Info 2024-Jul-11 16:03:03] ------------------------------------------------------------------------------
[PB Info 2024-Jul-11 16:03:03] || Program: Sorting Phase-II ||
[PB Info 2024-Jul-11 16:03:03] || Version: 4.3.1-1 ||
[PB Info 2024-Jul-11 16:03:03] || Start Time: Thu Jul 11 16:02:58 2024 ||
[PB Info 2024-Jul-11 16:03:03] || End Time: Thu Jul 11 16:03:03 2024 ||
[PB Info 2024-Jul-11 16:03:03] || Total Time: 5 seconds ||
[PB Info 2024-Jul-11 16:03:03] ------------------------------------------------------------------------------
[PB Info 2024-Jul-11 16:03:03] ------------------------------------------------------------------------------
[PB Info 2024-Jul-11 16:03:03] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Jul-11 16:03:03] || Version 4.3.1-1 ||
[PB Info 2024-Jul-11 16:03:03] || Marking Duplicates, BQSR ||
[PB Info 2024-Jul-11 16:03:03] ------------------------------------------------------------------------------
[PB Info 2024-Jul-11 16:03:03] CuBamWriter using CUDA device 2
[PB Info 2024-Jul-11 16:03:05] Using PBCuBamWriter for BAM writing (algo 0)
[PB Info 2024-Jul-11 16:03:05] progressMeter - Percentage
[PB Info 2024-Jul-11 16:03:15] 100.0
[PB Info 2024-Jul-11 16:03:16] BQSR and writing final BAM: 10.723 seconds
[PB Info 2024-Jul-11 16:03:16] ------------------------------------------------------------------------------
[PB Info 2024-Jul-11 16:03:16] || Program: Marking Duplicates, BQSR ||
[PB Info 2024-Jul-11 16:03:16] || Version: 4.3.1-1 ||
[PB Info 2024-Jul-11 16:03:16] || Start Time: Thu Jul 11 16:03:03 2024 ||
[PB Info 2024-Jul-11 16:03:16] || End Time: Thu Jul 11 16:03:16 2024 ||
[PB Info 2024-Jul-11 16:03:16] || Total Time: 13 seconds ||
[PB Info 2024-Jul-11 16:03:16] ------------------------------------------------------------------------------
real 3m16.856s
user 105m42.950s
sys 0m54.351s
nvidia-smi
