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fq2bam.sh.job_id.out
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Tue Feb 7 16:56:48 EST 2023
c1103a-s11.ufhpc
/home/hju/run_parabricks/dryrun
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /blue/vendor-
nvidia/hju/data_parabricks/parabricks_sample/Data/sample_1.fq.gz and /blue/vendor-
nvidia/hju/data_parabricks/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-Feb-07 16:56:53] ------------------------------------------------------------------------------
[PB Info 2023-Feb-07 16:56:53] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2023-Feb-07 16:56:53] || Version 4.0.1-1 ||
[PB Info 2023-Feb-07 16:56:53] || GPU-BWA mem, Sorting Phase-I ||
[PB Info 2023-Feb-07 16:56:53] ------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[PB Info 2023-Feb-07 16:56:56] GPU-BWA mem
[PB Info 2023-Feb-07 16:56:56] ProgressMeter Reads Base Pairs Aligned
[PB Info 2023-Feb-07 16:57:07] 5043564 570000000
[PB Info 2023-Feb-07 16:57:10] 10087128 1180000000
[PB Info 2023-Feb-07 16:57:14] 15130692 1760000000
[PB Info 2023-Feb-07 16:57:17] 20174256 2310000000
[PB Info 2023-Feb-07 16:57:21] 25217820 2900000000
[PB Info 2023-Feb-07 16:57:25] 30261384 3530000000
[PB Info 2023-Feb-07 16:57:28] 35304948 4050000000
[PB Info 2023-Feb-07 16:57:31] 40348512 4670000000
[PB Info 2023-Feb-07 16:57:35] 45392076 5220000000
[PB Info 2023-Feb-07 16:57:38] 50435640 5810000000
[PB Info 2023-Feb-07 16:59:45]
GPU-BWA Mem time: 168.868550 seconds
[PB Info 2023-Feb-07 16:59:45] GPU-BWA Mem is finished.
[main] CMD: /usr/local/parabricks/binaries//bin/bwa mem -Z ./pbOpts.txt /blue/vendor-nvidia/hju/data_parabricks/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta /blue/vendor-nvidia/hju/data_parabricks/parabricks_sample/Data/sample_1.fq.gz /blue/vendor-nvidia/hju/data_parabricks/parabricks_sample/Data/sample_2.fq.gz @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
[main] Real time: 171.776 sec; CPU: 1641.234 sec
[PB Info 2023-Feb-07 16:59:45] ------------------------------------------------------------------------------
[PB Info 2023-Feb-07 16:59:45] || Program: GPU-BWA mem, Sorting Phase-I ||
[PB Info 2023-Feb-07 16:59:45] || Version: 4.0.1-1 ||
[PB Info 2023-Feb-07 16:59:45] || Start Time: Tue Feb 7 16:56:53 2023 ||
[PB Info 2023-Feb-07 16:59:45] || End Time: Tue Feb 7 16:59:45 2023 ||
[PB Info 2023-Feb-07 16:59:45] || Total Time: 2 minutes 52 seconds ||
[PB Info 2023-Feb-07 16:59:45] ------------------------------------------------------------------------------
[PB Info 2023-Feb-07 16:59:49] ------------------------------------------------------------------------------
[PB Info 2023-Feb-07 16:59:49] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2023-Feb-07 16:59:49] || Version 4.0.1-1 ||
[PB Info 2023-Feb-07 16:59:49] || Sorting Phase-II ||
[PB Info 2023-Feb-07 16:59:49] ------------------------------------------------------------------------------
[PB Info 2023-Feb-07 16:59:49] progressMeter - Percentage
[PB Info 2023-Feb-07 16:59:49] 0.0 0.00 GB
[PB Info 2023-Feb-07 16:59:59] 60.2 2.00 GB
[PB Info 2023-Feb-07 17:00:09] Sorting and Marking: 20.001 seconds
[PB Info 2023-Feb-07 17:00:09] ------------------------------------------------------------------------------
[PB Info 2023-Feb-07 17:00:09] || Program: Sorting Phase-II ||
[PB Info 2023-Feb-07 17:00:09] || Version: 4.0.1-1 ||
[PB Info 2023-Feb-07 17:00:09] || Start Time: Tue Feb 7 16:59:49 2023 ||
[PB Info 2023-Feb-07 17:00:09] || End Time: Tue Feb 7 17:00:09 2023 ||
[PB Info 2023-Feb-07 17:00:09] || Total Time: 20 seconds ||
[PB Info 2023-Feb-07 17:00:09] ------------------------------------------------------------------------------
[PB Info 2023-Feb-07 17:00:09] ------------------------------------------------------------------------------
[PB Info 2023-Feb-07 17:00:09] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2023-Feb-07 17:00:09] || Version 4.0.1-1 ||
[PB Info 2023-Feb-07 17:00:09] || Marking Duplicates, BQSR ||
[PB Info 2023-Feb-07 17:00:09] ------------------------------------------------------------------------------
[PB Info 2023-Feb-07 17:00:09] progressMeter - Percentage
[PB Info 2023-Feb-07 17:00:19] 52.2 9.24 GB
[PB Info 2023-Feb-07 17:00:29] 100.0 0.00 GB
[PB Info 2023-Feb-07 17:00:29] BQSR and writing final BAM: 20.041 seconds
[PB Info 2023-Feb-07 17:00:29] ------------------------------------------------------------------------------
[PB Info 2023-Feb-07 17:00:29] || Program: Marking Duplicates, BQSR ||
[PB Info 2023-Feb-07 17:00:29] || Version: 4.0.1-1 ||
[PB Info 2023-Feb-07 17:00:29] || Start Time: Tue Feb 7 17:00:09 2023 ||
[PB Info 2023-Feb-07 17:00:29] || End Time: Tue Feb 7 17:00:29 2023 ||
[PB Info 2023-Feb-07 17:00:29] || Total Time: 20 seconds ||
[PB Info 2023-Feb-07 17:00:29] ------------------------------------------------------------------------------
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation