Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation [Parabricks Options Mesg]: Generating bed files from reference [Parabricks Options Mesg]: Read group created for /Parabricks/parabricks_sample/Data/sample_1.fq.gz and /Parabricks/parabricks_sample/Data/sample_2.fq.gz [Parabricks Options Mesg]: @RG\tID:sample1\tLB:lib1\tPL:PL1\tSM:sample1\tPU:unit1 WARNING: While bind mounting '/Parabricks/parabricks_sample': destination is already in the mount point list WARNING: While bind mounting '/Parabricks/parabricks_sample/Data:/Parabricks/parabricks_sample': destination is already in the mount point list [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Read group created for /Parabricks/parabricks_sample/Data/sample_1.fq.gz and /Parabricks/parabricks_sample/Data/sample_2.fq.gz [Parabricks Options Mesg]: @RG\tID:sample1\tLB:lib1\tPL:PL1\tSM:sample1\tPU:unit1 ------------------------------------------------------------------------------ || Parabricks accelerated Genomics Pipeline || || Version 3.6.1-1.ampere || || GPU-BWA mem, Sorting Phase-I || || Contact: Parabricks-Support@nvidia.com || ------------------------------------------------------------------------------ [M::bwa_idx_load_from_disk] read 0 ALT contigs GPU-BWA mem ProgressMeter Reads Base Pairs Aligned [09:33:07] 5043564 350000000 [09:33:09] 10087128 1110000000 [09:33:11] 15130692 1780000000 [09:33:13] 20174256 2330000000 [09:33:15] 25217820 2890000000 [09:33:18] 30261384 3470000000 [09:33:20] 35304948 4080000000 [09:33:23] 40348512 4680000000 [09:33:25] 45392076 5230000000 [09:33:28] 50435640 5840000000 GPU-BWA Mem time: 51.362389 seconds GPU-BWA Mem is finished. GPU Sorting, Marking Dups, BQSR ProgressMeter SAM Entries Completed Total GPU-BWA Mem + Sorting + MarkingDups + BQSR Generation + BAM writing Processing time: 51.364243 seconds [main] CMD: PARABRICKS mem -Z ./pbOpts.txt /Parabricks/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta /Parabricks/parabricks_sample/Data/sample_1.fq.gz /Parabricks/parabricks_sample/Data/sample_2.fq.gz @RG\tID:sample1\tLB:lib1\tPL:PL1\tSM:sample1\tPU:unit1 [main] Real time: 54.057 sec; CPU: 1549.371 sec ------------------------------------------------------------------------------ || Program: GPU-BWA mem, Sorting Phase-I || || Version: 3.6.1-1.ampere || || Start Time: Fri Nov 12 09:32:42 2021 || || End Time: Fri Nov 12 09:33:38 2021 || || Total Time: 56 seconds || ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ || Parabricks accelerated Genomics Pipeline || || Version 3.6.1-1.ampere || || Sorting Phase-II || || Contact: Parabricks-Support@nvidia.com || ------------------------------------------------------------------------------ progressMeter - Percentage [09:33:40] 0.0 0.00 GB Sorting and Marking: 10.000 seconds ------------------------------------------------------------------------------ || Program: Sorting Phase-II || || Version: 3.6.1-1.ampere || || Start Time: Fri Nov 12 09:33:40 2021 || || End Time: Fri Nov 12 09:33:50 2021 || || Total Time: 10 seconds || ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ || Parabricks accelerated Genomics Pipeline || || Version 3.6.1-1.ampere || || Marking Duplicates, BQSR || || Contact: Parabricks-Support@nvidia.com || ------------------------------------------------------------------------------ progressMeter - Percentage [09:34:33] 0.0 19.38 GB [09:34:43] 0.0 19.38 GB [09:34:53] 27.9 13.86 GB [09:35:03] 78.8 3.12 GB [09:35:13] 100.0 0.00 GB BQSR and writing final BAM: 50.243 seconds ------------------------------------------------------------------------------ || Program: Marking Duplicates, BQSR || || Version: 3.6.1-1.ampere || || Start Time: Fri Nov 12 09:33:50 2021 || || End Time: Fri Nov 12 09:35:14 2021 || || Total Time: 1 minute 24 seconds || ------------------------------------------------------------------------------ WARNING: While bind mounting '/Parabricks/parabricks_sample': destination is already in the mount point list WARNING: While bind mounting '/Parabricks/parabricks_sample/Data:/Parabricks/parabricks_sample': destination is already in the mount point list ------------------------------------------------------------------------------ || Parabricks accelerated Genomics Pipeline || || Version 3.6.1-1.ampere || || GPU-GATK4 HaplotypeCaller || || Contact: Parabricks-Support@nvidia.com || ------------------------------------------------------------------------------ [PB Info 2021-Nov-12 09:35:32] 0 /Parabricks/parabricks_sample/sample1.cram/Parabricks/parabricks_sample/sample1.par.g_non_xy.vcf [PB Info 2021-Nov-12 09:35:54] ProgressMeter - Current-Locus Elapsed-Minutes Regions-Processed Regions/Minute [PB Info 2021-Nov-12 09:36:04] chr1:45144148 0.2 191744 1150458 [PB Info 2021-Nov-12 09:36:14] chr1:118893332 0.3 502835 1508496 [PB Info 2021-Nov-12 09:36:24] chr1:200311249 0.5 756260 1512516 [PB Info 2021-Nov-12 09:36:34] chr2:24763066 0.7 1062365 1593547 [PB Info 2021-Nov-12 09:36:44] chr2:67622560 0.8 1244339 1493206 [PB Info 2021-Nov-12 09:36:54] chr2:104654216 1.0 1384619 1384619 [PB Info 2021-Nov-12 09:37:04] chr2:137174304 1.2 1519788 1302675 [PB Info 2021-Nov-12 09:37:14] chr2:145113532 1.3 1552904 1164678 [PB Info 2021-Nov-12 09:37:24] chr2:145113532 1.5 1552904 1035269 [PB Info 2021-Nov-12 09:37:34] chr2:175196469 1.7 1678788 1007272 [PB Info 2021-Nov-12 09:37:44] chr3:72843344 1.8 2271833 1239178 [PB Info 2021-Nov-12 09:37:54] chr4:13017512 2.0 2840417 1420208 [PB Info 2021-Nov-12 09:38:04] chr4:165282901 2.2 3466393 1599873 [PB Info 2021-Nov-12 09:38:14] chr5:126873400 2.3 4075729 1746741 [PB Info 2021-Nov-12 09:38:24] chr6:21517801 2.5 4399258 1759703 [PB Info 2021-Nov-12 09:38:34] chr6:108634329 2.7 4737130 1776421 [PB Info 2021-Nov-12 09:38:44] chr7:98999909 2.8 5397712 1905074 [PB Info 2021-Nov-12 09:38:54] chr8:37094152 3.0 5797801 1932600 [PB Info 2021-Nov-12 09:39:04] chr9:4422897 3.2 6257914 1976181 [PB Info 2021-Nov-12 09:39:14] chr10:36167781 3.3 6888046 2066413 [PB Info 2021-Nov-12 09:39:24] chr11:73166117 3.5 7586258 2167502 [PB Info 2021-Nov-12 09:39:34] chr12:108090912 3.7 8290641 2261083 [PB Info 2021-Nov-12 09:39:44] chr14:60907194 3.8 8987309 2344515 [PB Info 2021-Nov-12 09:39:54] chr14:76924598 4.0 9056210 2264052 [PB Info 2021-Nov-12 09:40:04] chr15:84683215 4.2 9425878 2262210 [PB Info 2021-Nov-12 09:40:14] chr17:40291099 4.3 9976166 2302192 [PB Info 2021-Nov-12 09:40:24] chr19:44370932 4.5 10646274 2365838 [PB Info 2021-Nov-12 09:40:34] chr11_JH159137v1_alt:32716 4.7 11338400 2429657 [PB Info 2021-Nov-12 09:40:48] Total time taken: 316.084843 ------------------------------------------------------------------------------ || Program: GPU-GATK4 HaplotypeCaller || || Version: 3.6.1-1.ampere || || Start Time: Fri Nov 12 09:35:18 2021 || || End Time: Fri Nov 12 09:40:48 2021 || || Total Time: 5 minutes 30 seconds || ------------------------------------------------------------------------------ WARNING: While bind mounting '/Parabricks/parabricks_sample': destination is already in the mount point list WARNING: While bind mounting '/Parabricks/parabricks_sample/Data:/Parabricks/parabricks_sample': destination is already in the mount point list Traceback (most recent call last): File "/parabricks/run_pipeline.py", line 7, in sys.exit(PB.pb_main()) File "PB.pyx", line 1710, in PB.pb_main File "/parabricks/pbargs_check.py", line 550, in pbargs_check check_haplotypecaller(runArgs.runArgs) File "/parabricks/pbargs_check.py", line 179, in check_haplotypecaller check_human_par(runArgs) File "/parabricks/pbargs_check.py", line 76, in check_human_par chrom_reads = f.readlines() File "/usr/lib/python3.7/codecs.py", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0x83 in position 26: invalid start byte Could not run haplotypecaller as part of human par germline pipeline Exiting pbrun ...