[log] germline: WGS + AWS: g4dn.4xlarge (T4 + 16vCPU + 64GB) === ###### tags: `Parabricks-v3.8` ###### tags: `基因體`, `NVIDIA`, `Clara`, `Parabricks`, `二級分析` <br> [TOC] <br> ## 硬體資源：EC2 / g4dn.4xlarge > 查閱方式：[[HackMD] AWS / 容器執行個體(EC2) / EC2 / g4dn.4xlarge](https://hackmd.io/QavypnMBRoW8P9aH4gw8FA#EC2--g4dnxlarge) [![](https://i.imgur.com/7mWwSMW.png)](https://i.imgur.com/7mWwSMW.png) ### GPU - GPU 0: Tesla T4 (15360MiB) ### CPU - Intel® Xeon® Platinum 8259CL CPU @ 2.50GHz - 1(插槽) x 8(核/插槽) x 2(超執行緒/核) = 16條執行緒 (16vCPU) - CPU MHz: 3114 - BogoMIPS: 5000 - :::spoiler `$ lscpu` ``` $ lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 16 On-line CPU(s) list: 0-15 Thread(s) per core: 2 Core(s) per socket: 8 Socket(s): 1 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 85 Model name: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz Stepping: 7 CPU MHz: 3113.942 <--- 會一直變動 BogoMIPS: 4999.99 Hypervisor vendor: KVM Virtualization type: full L1d cache: 32K L1i cache: 32K L2 cache: 1024K L3 cache: 36608K NUMA node0 CPU(s): 0-15 Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single pti fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves ida arat pku ospke avx512_vnni ``` ::: ### RAM - 64GB ### Storage - **規格**：`General Purpose SSD (gp3)`, `3000IOPS` - **儲存容量** - `/`: 50GB - `/workspace`: 500GB - **實際效能測試** | | 速度 | IOPS | |---|-----|------| | Read | 8.8 MiB/s | 2252 | | Write | 2.94 MiB/s | 752 | ```bash= $ apt-get install -y fio $ fio \ --randrepeat=1 \ --ioengine=libaio \ --direct=1 \ --gtod_reduce=1 \ --name=fiotest \ --filename=testfio \ --bs=4k \ --iodepth=64 \ --size=8G \ --readwrite=randrw \ --rwmixread=75 ``` :::spoiler 點此查看 **執行結果** ``` fiotest: (g=0): rw=randrw, bs=(R) 4096B-4096B, (W) 4096B-4096B, (T) 4096B-4096B, ioengine=libaio, iodepth=64 fio-3.1 Starting 1 process fiotest: Laying out IO file (1 file / 8192MiB) Jobs: 1 (f=1): [m(1)][100.0%][r=9021KiB/s,w=2982KiB/s][r=2255,w=745 IOPS][eta 00m:00s] fiotest: (groupid=0, jobs=1): err= 0: pid=14500: Fri Mar 18 01:33:50 2022 read: IOPS=2252, BW=9009KiB/s (9225kB/s)(6141MiB/698043msec) bw ( KiB/s): min= 8600, max=26552, per=100.00%, avg=9008.19, stdev=489.47, samples=1396 iops : min= 2150, max= 6638, avg=2252.04, stdev=122.37, samples=1396 write: IOPS=752, BW=3008KiB/s (3081kB/s)(2051MiB/698043msec) bw ( KiB/s): min= 2520, max= 9200, per=100.00%, avg=3008.15, stdev=215.20, samples=1396 iops : min= 630, max= 2300, avg=752.02, stdev=53.80, samples=1396 cpu : usr=0.68%, sys=2.03%, ctx=691431, majf=0, minf=8 IO depths : 1=0.1%, 2=0.1%, 4=0.1%, 8=0.1%, 16=0.1%, 32=0.1%, >=64=100.0% submit : 0=0.0%, 4=100.0%, 8=0.0%, 16=0.0%, 32=0.0%, 64=0.0%, >=64=0.0% complete : 0=0.0%, 4=100.0%, 8=0.0%, 16=0.0%, 32=0.0%, 64=0.1%, >=64=0.0% issued rwt: total=1572145,525007,0, short=0,0,0, dropped=0,0,0 latency : target=0, window=0, percentile=100.00%, depth=64 Run status group 0 (all jobs): READ: bw=9009KiB/s (9225kB/s), 9009KiB/s-9009KiB/s (9225kB/s-9225kB/s), io=6141MiB (6440MB), run=698043-698043msec WRITE: bw=3008KiB/s (3081kB/s), 3008KiB/s-3008KiB/s (3081kB/s-3081kB/s), io=2051MiB (2150MB), run=698043-698043msec Disk stats (read/write): nvme2n1: ios=1571732/524908, merge=0/23, ticks=15631663/5277839, in_queue=16745612, util=100.00% ``` ::: <br> <hr> <br> ## script ```bash= # cmd: sh germline.sh 2>&1 | tee germline.sh.log & date && start_time=`date +%s` && echo "start_time:" $start_time pbrun germline \ --ref parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \ --in-fq \ datasets/WGS-LIS-AI018A_R1.fastq.gz \ datasets/WGS-LIS-AI018A_R2.fastq.gz \ --knownSites parabricks_sample/Ref/Homo_sapiens_assembly38.known_indels.vcf.gz \ --out-bam output/output.bam \ --out-variants output/output.vcf \ --out-recal-file output/report.txt; \ echo "exit code:" $!; \ echo "Done!" date && end_time=`date +%s` && echo "end_time:" $end_time total=$((end_time - start_time)) time_h=$((total/3600)) time_m=$(( (total - time_h*3600) / 60 )) time_s=$(( total - time_h*3600 - time_m*60 )) echo "Total time: ${time_h}h ${time_m}m ${time_s}s" ``` <br> <hr> <br> ## Log > **g4dn.4xlarge (T4 + 16vCPU + 64GB)** | Programs | Round-1 | Round-2 | Average | |----------|--------:|--------:|--------:| | GPU-BWA mem, Sorting Phase-I | 4h 55m 30s | 4h 55m 45s | 4h 55m 38s | | Sorting Phase-II | 5m 40s | 5m 41s | 5m 40s | | Marking Dmuplicates, BQSR | 29m 30s | 29m 46s | 29m 38s | | GPU-GATK4 HaplotypeCaller | 62m 29s | 62m 48s | 62m 38s | | | | | | **Total** | 6h 33m 31s | 6h 34m 08s | 6h 33m 50s | ```= $ sh germline.sh 2>&1 | tee germline.sh.log & [1] 5789 Thu Mar 17 06:49:22 UTC 2022 start_time: 1647499762 Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /workspace/datasets/WGS-LIS-AI018A_R1.fastq.gz and /workspace/datasets/WGS-LIS-AI018A_R2.fastq.gz [Parabricks Options Mesg]: @RG\tID:H3WFJDSXX.1\tLB:lib1\tPL:bar\tSM:sample\tPU:H3WFJDSXX.1 [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Read group created for /workspace/datasets/WGS-LIS-AI018A_R1.fastq.gz and /workspace/datasets/WGS-LIS-AI018A_R2.fastq.gz [Parabricks Options Mesg]: @RG\tID:H3WFJDSXX.1\tLB:lib1\tPL:bar\tSM:sample\tPU:H3WFJDSXX.1 [PB Info 2022-Mar-17 06:49:23] Logger not initialized! [PB Info 2022-Mar-17 06:49:23] ------------------------------------------------------------------------------ [PB Info 2022-Mar-17 06:49:23] || Parabricks accelerated Genomics Pipeline || [PB Info 2022-Mar-17 06:49:23] || Version 3.7.0-1 || [PB Info 2022-Mar-17 06:49:23] || GPU-BWA mem, Sorting Phase-I || [PB Info 2022-Mar-17 06:49:23] || Contact: Parabricks-Support@nvidia.com || [PB Info 2022-Mar-17 06:49:23] ------------------------------------------------------------------------------ gpg: keyblock resource '/home/ubuntu/.gnupg/pubring.kbx': Permission denied [PB Info 2022-Mar-17 06:49:23] Logger already initialized, continuing with current settings. [M::bwa_idx_load_from_disk] read 0 ALT contigs [PB Warning 2022-Mar-17 06:50:07][ParaBricks/src/pbOpts.cu:316] WARNING The system has 62 GB, however recommended RAM with 1 GPU is 64 GB. The run might not finish or might have less than expected performance. [PB Info 2022-Mar-17 06:50:07] GPU-BWA mem [PB Info 2022-Mar-17 06:50:07] ProgressMeter Reads Base Pairs Aligned (base) ubuntu@ip-172-31-17-84:/workspace$ [PB Info 2022-Mar-17 06:51:42] 5033176 760000000 [PB Info 2022-Mar-17 06:53:14] 10066352 1520000000 [PB Info 2022-Mar-17 06:54:46] 15099528 2280000000 [PB Info 2022-Mar-17 06:56:21] 20132704 3040000000 [PB Info 2022-Mar-17 06:57:58] 25165880 3800000000 [PB Info 2022-Mar-17 06:59:36] 30199056 4560000000 [PB Info 2022-Mar-17 07:01:13] 35232232 5320000000 [PB Info 2022-Mar-17 07:02:51] 40265408 6080000000 [PB Info 2022-Mar-17 07:04:31] 45298584 6840000000 [PB Info 2022-Mar-17 07:06:06] 50331760 7600000000 [PB Info 2022-Mar-17 07:07:38] 55364936 8360000000 [PB Info 2022-Mar-17 07:09:13] 60398112 9120000000 [PB Info 2022-Mar-17 07:10:47] 65431288 9880000000 [PB Info 2022-Mar-17 07:12:20] 70464464 10640000000 [PB Info 2022-Mar-17 07:13:54] 75497640 11400000000 [PB Info 2022-Mar-17 07:15:29] 80530816 12160000000 [PB Info 2022-Mar-17 07:17:04] 85563992 12920000000 [PB Info 2022-Mar-17 07:18:39] 90597168 13680000000 [PB Info 2022-Mar-17 07:20:12] 95630344 14440000000 [PB Info 2022-Mar-17 07:21:47] 100663520 15200000000 [PB Info 2022-Mar-17 07:23:23] 105696696 15960000000 [PB Info 2022-Mar-17 07:25:00] 110729872 16720000000 [PB Info 2022-Mar-17 07:26:35] 115763048 17480000000 [PB Info 2022-Mar-17 07:28:08] 120796224 18240000000 [PB Info 2022-Mar-17 07:29:41] 125829400 19000000000 [PB Info 2022-Mar-17 07:31:12] 130862576 19760000000 [PB Info 2022-Mar-17 07:32:45] 135895752 20520000000 [PB Info 2022-Mar-17 07:34:22] 140928928 21280000000 [PB Info 2022-Mar-17 07:35:59] 145962104 22040000000 [PB Info 2022-Mar-17 07:37:32] 150995280 22800000000 [PB Info 2022-Mar-17 07:39:05] 156028456 23560000000 [PB Info 2022-Mar-17 07:40:44] 161061632 24320000000 [PB Info 2022-Mar-17 07:42:23] 166094808 25080000000 [PB Info 2022-Mar-17 07:44:00] 171127984 25840000000 [PB Info 2022-Mar-17 07:45:36] 176161160 26600000000 [PB Info 2022-Mar-17 07:47:13] 181194336 27360000000 [PB Info 2022-Mar-17 07:48:50] 186227512 28120000000 [PB Info 2022-Mar-17 07:50:25] 191260688 28880000000 [PB Info 2022-Mar-17 07:51:59] 196293864 29640000000 [PB Info 2022-Mar-17 07:53:36] 201327040 30400000000 [PB Info 2022-Mar-17 07:55:15] 206360216 31160000000 [PB Info 2022-Mar-17 07:56:52] 211393392 31920000000 [PB Info 2022-Mar-17 07:58:30] 216426568 32680000000 [PB Info 2022-Mar-17 08:00:09] 221459744 33440000000 [PB Info 2022-Mar-17 08:01:42] 226492920 34200000000 [PB Info 2022-Mar-17 08:03:14] 231526096 34960000000 [PB Info 2022-Mar-17 08:04:50] 236559272 35720000000 [PB Info 2022-Mar-17 08:06:24] 241592448 36480000000 [PB Info 2022-Mar-17 08:07:57] 246625624 37240000000 [PB Info 2022-Mar-17 08:09:30] 251658800 38000000000 [PB Info 2022-Mar-17 08:11:03] 256691976 38760000000 [PB Info 2022-Mar-17 08:12:36] 261725152 39520000000 [PB Info 2022-Mar-17 08:14:11] 266758328 40280000000 [PB Info 2022-Mar-17 08:15:50] 271791504 41040000000 [PB Info 2022-Mar-17 08:17:29] 276824680 41800000000 [PB Info 2022-Mar-17 08:19:07] 281857856 42560000000 [PB Info 2022-Mar-17 08:20:42] 286891032 43320000000 [PB Info 2022-Mar-17 08:22:15] 291924208 44080000000 [PB Info 2022-Mar-17 08:23:49] 296957384 44840000000 [PB Info 2022-Mar-17 08:25:25] 301990560 45600000000 [PB Info 2022-Mar-17 08:26:58] 307023736 46360000000 [PB Info 2022-Mar-17 08:28:33] 312056912 47120000000 [PB Info 2022-Mar-17 08:30:07] 317090088 47880000000 [PB Info 2022-Mar-17 08:31:39] 322123264 48640000000 [PB Info 2022-Mar-17 08:33:13] 327156440 49400000000 [PB Info 2022-Mar-17 08:34:50] 332189616 50160000000 [PB Info 2022-Mar-17 08:36:22] 337222792 50920000000 [PB Info 2022-Mar-17 08:37:54] 342255968 51680000000 [PB Info 2022-Mar-17 08:39:31] 347289144 52440000000 [PB Info 2022-Mar-17 08:41:09] 352322320 53200000000 [PB Info 2022-Mar-17 08:42:42] 357355496 53960000000 [PB Info 2022-Mar-17 08:44:14] 362388672 54720000000 [PB Info 2022-Mar-17 08:45:47] 367421848 55480000000 [PB Info 2022-Mar-17 08:47:22] 372455024 56240000000 [PB Info 2022-Mar-17 08:48:57] 377488200 57000000000 [PB Info 2022-Mar-17 08:50:29] 382521376 57760000000 [PB Info 2022-Mar-17 08:52:05] 387554552 58520000000 [PB Info 2022-Mar-17 08:53:38] 392587728 59280000000 [PB Info 2022-Mar-17 08:55:12] 397620904 60040000000 [PB Info 2022-Mar-17 08:56:44] 402654080 60800000000 [PB Info 2022-Mar-17 08:58:16] 407687256 61560000000 [PB Info 2022-Mar-17 08:59:50] 412720432 62320000000 [PB Info 2022-Mar-17 09:01:26] 417753608 63080000000 [PB Info 2022-Mar-17 09:03:02] 422786784 63840000000 [PB Info 2022-Mar-17 09:04:39] 427819960 64600000000 [PB Info 2022-Mar-17 09:06:12] 432853136 65360000000 [PB Info 2022-Mar-17 09:07:44] 437886312 66120000000 [PB Info 2022-Mar-17 09:09:15] 442919488 66880000000 [PB Info 2022-Mar-17 09:10:47] 447952664 67640000000 [PB Info 2022-Mar-17 09:12:21] 452985840 68400000000 [PB Info 2022-Mar-17 09:13:57] 458019016 69160000000 [PB Info 2022-Mar-17 09:15:31] 463052192 69920000000 [PB Info 2022-Mar-17 09:17:05] 468085368 70680000000 [PB Info 2022-Mar-17 09:18:40] 473118544 71440000000 [PB Info 2022-Mar-17 09:20:17] 478151720 72200000000 [PB Info 2022-Mar-17 09:21:50] 483184896 72960000000 [PB Info 2022-Mar-17 09:23:28] 488218072 73720000000 [PB Info 2022-Mar-17 09:25:06] 493251248 74480000000 [PB Info 2022-Mar-17 09:26:44] 498284424 75240000000 [PB Info 2022-Mar-17 09:28:18] 503317600 76000000000 [PB Info 2022-Mar-17 09:29:52] 508350776 76760000000 [PB Info 2022-Mar-17 09:31:29] 513383952 77520000000 [PB Info 2022-Mar-17 09:33:08] 518417128 78280000000 [PB Info 2022-Mar-17 09:34:45] 523450304 79040000000 [PB Info 2022-Mar-17 09:36:25] 528483480 79800000000 [PB Info 2022-Mar-17 09:38:01] 533516656 80560000000 [PB Info 2022-Mar-17 09:39:38] 538549832 81320000000 [PB Info 2022-Mar-17 09:41:15] 543583008 82080000000 [PB Info 2022-Mar-17 09:42:53] 548616184 82840000000 [PB Info 2022-Mar-17 09:44:32] 553649360 83600000000 [PB Info 2022-Mar-17 09:46:08] 558682536 84360000000 [PB Info 2022-Mar-17 09:47:48] 563715712 85120000000 [PB Info 2022-Mar-17 09:49:26] 568748888 85880000000 [PB Info 2022-Mar-17 09:51:04] 573782064 86640000000 [PB Info 2022-Mar-17 09:52:38] 578815240 87400000000 [PB Info 2022-Mar-17 09:54:13] 583848416 88160000000 [PB Info 2022-Mar-17 09:55:48] 588881592 88920000000 [PB Info 2022-Mar-17 09:57:23] 593914768 89680000000 [PB Info 2022-Mar-17 09:59:00] 598947944 90440000000 [PB Info 2022-Mar-17 10:00:39] 603981120 91200000000 [PB Info 2022-Mar-17 10:02:16] 609014296 91960000000 [PB Info 2022-Mar-17 10:03:56] 614047472 92720000000 [PB Info 2022-Mar-17 10:05:30] 619080648 93480000000 [PB Info 2022-Mar-17 10:07:03] 624113824 94240000000 [PB Info 2022-Mar-17 10:08:35] 629147000 95000000000 [PB Info 2022-Mar-17 10:10:06] 634180176 95760000000 [PB Info 2022-Mar-17 10:11:38] 639213352 96520000000 [PB Info 2022-Mar-17 10:13:11] 644246528 97280000000 [PB Info 2022-Mar-17 10:14:47] 649279704 98040000000 [PB Info 2022-Mar-17 10:16:26] 654312880 98800000000 [PB Info 2022-Mar-17 10:18:01] 659346056 99560000000 [PB Info 2022-Mar-17 10:19:37] 664379232 100320000000 [PB Info 2022-Mar-17 10:21:08] 669412408 101080000000 [PB Info 2022-Mar-17 10:22:40] 674445584 101840000000 [PB Info 2022-Mar-17 10:24:13] 679478760 102600000000 [PB Info 2022-Mar-17 10:25:48] 684511936 103360000000 [PB Info 2022-Mar-17 10:27:23] 689545112 104120000000 [PB Info 2022-Mar-17 10:28:58] 694578288 104880000000 [PB Info 2022-Mar-17 10:30:36] 699611464 105640000000 [PB Info 2022-Mar-17 10:32:14] 704644640 106400000000 [PB Info 2022-Mar-17 10:33:51] 709677816 107160000000 [PB Info 2022-Mar-17 10:35:27] 714710992 107920000000 [PB Info 2022-Mar-17 10:37:00] 719744168 108680000000 [PB Info 2022-Mar-17 10:38:33] 724777344 109440000000 [PB Info 2022-Mar-17 10:40:10] 729810520 110200000000 [PB Info 2022-Mar-17 10:41:46] 734843696 110960000000 [PB Info 2022-Mar-17 10:43:24] 739876872 111720000000 [PB Info 2022-Mar-17 10:45:01] 744910048 112480000000 [PB Info 2022-Mar-17 10:46:38] 749943224 113240000000 [PB Info 2022-Mar-17 10:48:15] 754976400 114000000000 [PB Info 2022-Mar-17 10:49:53] 760009576 114760000000 [PB Info 2022-Mar-17 10:51:30] 765042752 115520000000 [PB Info 2022-Mar-17 10:53:06] 770075928 116280000000 [PB Info 2022-Mar-17 10:54:38] 775109104 117040000000 [PB Info 2022-Mar-17 10:56:13] 780142280 117800000000 [PB Info 2022-Mar-17 10:57:49] 785175456 118560000000 [PB Info 2022-Mar-17 10:59:27] 790208632 119320000000 [PB Info 2022-Mar-17 11:01:03] 795241808 120080000000 [PB Info 2022-Mar-17 11:02:42] 800274984 120840000000 [PB Info 2022-Mar-17 11:04:21] 805308160 121600000000 [PB Info 2022-Mar-17 11:05:55] 810341336 122360000000 [PB Info 2022-Mar-17 11:07:27] 815374512 123120000000 [PB Info 2022-Mar-17 11:09:00] 820407688 123880000000 [PB Info 2022-Mar-17 11:10:31] 825440864 124640000000 [PB Info 2022-Mar-17 11:12:04] 830474040 125400000000 [PB Info 2022-Mar-17 11:13:36] 835507216 126160000000 [PB Info 2022-Mar-17 11:15:12] 840540392 126920000000 [PB Info 2022-Mar-17 11:16:43] 845573568 127680000000 [PB Info 2022-Mar-17 11:18:17] 850606744 128440000000 [PB Info 2022-Mar-17 11:19:52] 855639920 129200000000 [PB Info 2022-Mar-17 11:21:30] 860673096 129960000000 [PB Info 2022-Mar-17 11:23:07] 865706272 130720000000 [PB Info 2022-Mar-17 11:24:43] 870739448 131480000000 [PB Info 2022-Mar-17 11:26:19] 875772624 132240000000 [PB Info 2022-Mar-17 11:27:58] 880805800 133000000000 [PB Info 2022-Mar-17 11:29:30] 885838976 133760000000 [PB Info 2022-Mar-17 11:31:02] 890872152 134520000000 [PB Info 2022-Mar-17 11:32:34] 895905328 135280000000 [PB Info 2022-Mar-17 11:34:08] 900938504 136040000000 [PB Info 2022-Mar-17 11:35:41] 905971680 136800000000 [PB Info 2022-Mar-17 11:37:14] 911004856 137560000000 [PB Info 2022-Mar-17 11:38:46] 916038032 138320000000 [PB Info 2022-Mar-17 11:40:21] 921071208 139080000000 [PB Info 2022-Mar-17 11:41:55] 926104384 139840000000 [PB Info 2022-Mar-17 11:43:27] 931137560 140600000000 [PB Info 2022-Mar-17 11:44:53] GPU-BWA Mem time: 17686.079019 seconds [PB Info 2022-Mar-17 11:44:53] GPU-BWA Mem is finished. [main] CMD: PARABRICKS mem -Z ./pbOpts.txt /workspace/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta /workspace/datasets/WGS-LIS-AI018A_R1.fastq.gz /workspace/datasets/WGS-LIS-AI018A_R2.fastq.gz @RG\tID:H3WFJDSXX.1\tLB:lib1\tPL:bar\tSM:sample\tPU:H3WFJDSXX.1 [main] Real time: 17729.759 sec; CPU: 185965.745 sec [PB Info 2022-Mar-17 11:44:53] ------------------------------------------------------------------------------ [PB Info 2022-Mar-17 11:44:53] || Program: GPU-BWA mem, Sorting Phase-I || [PB Info 2022-Mar-17 11:44:53] || Version: 3.7.0-1 || [PB Info 2022-Mar-17 11:44:53] || Start Time: Thu Mar 17 06:49:23 2022 || [PB Info 2022-Mar-17 11:44:53] || End Time: Thu Mar 17 11:44:53 2022 || [PB Info 2022-Mar-17 11:44:53] || Total Time: 295 minutes 30 seconds || [PB Info 2022-Mar-17 11:44:53] ------------------------------------------------------------------------------ [PB Info 2022-Mar-17 11:44:55] ------------------------------------------------------------------------------ [PB Info 2022-Mar-17 11:44:55] || Parabricks accelerated Genomics Pipeline || [PB Info 2022-Mar-17 11:44:55] || Version 3.7.0-1 || [PB Info 2022-Mar-17 11:44:55] || Sorting Phase-II || [PB Info 2022-Mar-17 11:44:55] || Contact: Parabricks-Support@nvidia.com || [PB Info 2022-Mar-17 11:44:55] ------------------------------------------------------------------------------ gpg: keyblock resource '/home/ubuntu/.gnupg/pubring.kbx': Permission denied [PB Info 2022-Mar-17 11:44:55] progressMeter - Percentage [PB Info 2022-Mar-17 11:44:55] 0.0 0.00 GB [PB Info 2022-Mar-17 11:45:05] 0.0 3.00 GB [PB Info 2022-Mar-17 11:45:15] 3.7 3.00 GB [PB Info 2022-Mar-17 11:45:25] 8.0 3.00 GB [PB Info 2022-Mar-17 11:45:35] 12.0 3.00 GB [PB Info 2022-Mar-17 11:45:45] 15.8 3.00 GB [PB Info 2022-Mar-17 11:45:55] 19.8 3.00 GB [PB Info 2022-Mar-17 11:46:05] 23.4 3.00 GB [PB Info 2022-Mar-17 11:46:15] 27.5 3.00 GB [PB Info 2022-Mar-17 11:46:25] 31.6 3.00 GB [PB Info 2022-Mar-17 11:46:35] 35.6 3.00 GB [PB Info 2022-Mar-17 11:46:45] 39.0 3.00 GB [PB Info 2022-Mar-17 11:46:55] 42.9 3.00 GB [PB Info 2022-Mar-17 11:47:05] 45.8 4.00 GB [PB Info 2022-Mar-17 11:47:15] 46.1 8.00 GB [PB Info 2022-Mar-17 11:47:25] 46.3 12.00 GB [PB Info 2022-Mar-17 11:47:35] 46.5 15.00 GB [PB Info 2022-Mar-17 11:47:45] 46.7 19.00 GB [PB Info 2022-Mar-17 11:47:55] 47.0 22.00 GB [PB Info 2022-Mar-17 11:48:05] 48.3 24.00 GB [PB Info 2022-Mar-17 11:48:15] 49.6 26.00 GB [PB Info 2022-Mar-17 11:48:25] 50.5 27.00 GB [PB Info 2022-Mar-17 11:48:35] 51.6 28.00 GB [PB Info 2022-Mar-17 11:48:45] 53.9 28.00 GB [PB Info 2022-Mar-17 11:48:55] 56.1 29.00 GB [PB Info 2022-Mar-17 11:49:05] 58.4 28.00 GB [PB Info 2022-Mar-17 11:49:15] 60.8 28.00 GB [PB Info 2022-Mar-17 11:49:25] 63.0 28.00 GB [PB Info 2022-Mar-17 11:49:35] 66.7 28.00 GB [PB Info 2022-Mar-17 11:49:45] 70.1 26.00 GB [PB Info 2022-Mar-17 11:49:55] 75.8 20.00 GB [PB Info 2022-Mar-17 11:50:05] 81.7 14.00 GB [PB Info 2022-Mar-17 11:50:15] 87.9 8.00 GB [PB Info 2022-Mar-17 11:50:25] 95.3 2.00 GB [PB Info 2022-Mar-17 11:50:35] Sorting and Marking: 340.005 seconds [PB Info 2022-Mar-17 11:50:35] ------------------------------------------------------------------------------ [PB Info 2022-Mar-17 11:50:35] || Program: Sorting Phase-II || [PB Info 2022-Mar-17 11:50:35] || Version: 3.7.0-1 || [PB Info 2022-Mar-17 11:50:35] || Start Time: Thu Mar 17 11:44:55 2022 || [PB Info 2022-Mar-17 11:50:35] || End Time: Thu Mar 17 11:50:35 2022 || [PB Info 2022-Mar-17 11:50:35] || Total Time: 5 minutes 40 seconds || [PB Info 2022-Mar-17 11:50:35] ------------------------------------------------------------------------------ [PB Info 2022-Mar-17 11:50:36] ------------------------------------------------------------------------------ [PB Info 2022-Mar-17 11:50:36] || Parabricks accelerated Genomics Pipeline || [PB Info 2022-Mar-17 11:50:36] || Version 3.7.0-1 || [PB Info 2022-Mar-17 11:50:36] || Marking Duplicates, BQSR || [PB Info 2022-Mar-17 11:50:36] || Contact: Parabricks-Support@nvidia.com || [PB Info 2022-Mar-17 11:50:36] ------------------------------------------------------------------------------ gpg: keyblock resource '/home/ubuntu/.gnupg/pubring.kbx': Permission denied [PB Info 2022-Mar-17 11:50:36] progressMeter - Percentage [PB Info 2022-Mar-17 11:50:46] 0.0 4.10 GB [PB Info 2022-Mar-17 11:50:56] 0.0 8.15 GB [PB Info 2022-Mar-17 11:51:06] 0.0 10.49 GB [PB Info 2022-Mar-17 11:51:16] 0.0 12.84 GB [PB Info 2022-Mar-17 11:51:26] 0.0 15.22 GB [PB Info 2022-Mar-17 11:51:36] 0.0 18.63 GB [PB Info 2022-Mar-17 11:51:46] 0.0 20.28 GB [PB Info 2022-Mar-17 11:51:56] 0.0 23.13 GB [PB Info 2022-Mar-17 11:52:06] 0.0 25.06 GB [PB Info 2022-Mar-17 11:52:16] 0.0 27.86 GB [PB Info 2022-Mar-17 11:52:26] 0.0 29.20 GB [PB Info 2022-Mar-17 11:52:36] 0.0 29.20 GB [PB Info 2022-Mar-17 11:52:46] 0.0 29.20 GB [PB Info 2022-Mar-17 11:52:56] 0.0 29.20 GB [PB Info 2022-Mar-17 11:53:06] 0.0 29.20 GB [PB Info 2022-Mar-17 11:53:16] 0.0 29.20 GB [PB Info 2022-Mar-17 11:53:26] 0.0 29.20 GB [PB Info 2022-Mar-17 11:53:36] 1.2 27.21 GB [PB Info 2022-Mar-17 11:53:46] 2.4 24.43 GB [PB Info 2022-Mar-17 11:53:56] 3.4 23.43 GB [PB Info 2022-Mar-17 11:54:06] 3.7 24.59 GB [PB Info 2022-Mar-17 11:54:16] 5.8 19.53 GB [PB Info 2022-Mar-17 11:54:26] 6.7 17.90 GB [PB Info 2022-Mar-17 11:54:36] 7.7 17.24 GB [PB Info 2022-Mar-17 11:54:46] 8.6 15.16 GB [PB Info 2022-Mar-17 11:54:56] 9.1 14.93 GB [PB Info 2022-Mar-17 11:55:06] 9.4 16.89 GB [PB Info 2022-Mar-17 11:55:16] 9.7 18.06 GB [PB Info 2022-Mar-17 11:55:26] 10.0 19.28 GB [PB Info 2022-Mar-17 11:55:36] 10.2 21.74 GB [PB Info 2022-Mar-17 11:55:46] 10.4 23.32 GB [PB Info 2022-Mar-17 11:55:56] 10.7 24.64 GB [PB Info 2022-Mar-17 11:56:06] 11.0 26.57 GB [PB Info 2022-Mar-17 11:56:16] 11.3 27.77 GB [PB Info 2022-Mar-17 11:56:26] 11.5 29.37 GB [PB Info 2022-Mar-17 11:56:36] 12.1 28.56 GB [PB Info 2022-Mar-17 11:56:46] 12.5 30.14 GB [PB Info 2022-Mar-17 11:56:56] 13.0 29.71 GB [PB Info 2022-Mar-17 11:57:06] 13.6 29.39 GB [PB Info 2022-Mar-17 11:57:16] 14.2 29.90 GB [PB Info 2022-Mar-17 11:57:26] 14.7 29.48 GB [PB Info 2022-Mar-17 11:57:36] 15.1 29.03 GB [PB Info 2022-Mar-17 11:57:46] 15.8 29.14 GB [PB Info 2022-Mar-17 11:57:56] 16.3 30.20 GB [PB Info 2022-Mar-17 11:58:06] 16.8 29.35 GB [PB Info 2022-Mar-17 11:58:16] 17.4 29.31 GB [PB Info 2022-Mar-17 11:58:26] 17.9 29.93 GB [PB Info 2022-Mar-17 11:58:36] 18.4 29.57 GB [PB Info 2022-Mar-17 11:58:46] 19.0 29.18 GB [PB Info 2022-Mar-17 11:58:56] 19.5 29.85 GB [PB Info 2022-Mar-17 11:59:06] 20.1 29.21 GB [PB Info 2022-Mar-17 11:59:16] 20.7 29.61 GB [PB Info 2022-Mar-17 11:59:26] 21.1 28.88 GB [PB Info 2022-Mar-17 11:59:36] 21.8 28.96 GB [PB Info 2022-Mar-17 11:59:46] 22.2 28.95 GB [PB Info 2022-Mar-17 11:59:56] 22.7 29.00 GB [PB Info 2022-Mar-17 12:00:06] 23.3 29.83 GB [PB Info 2022-Mar-17 12:00:16] 23.8 29.48 GB [PB Info 2022-Mar-17 12:00:26] 24.3 30.33 GB [PB Info 2022-Mar-17 12:00:36] 24.9 29.64 GB [PB Info 2022-Mar-17 12:00:46] 25.6 28.94 GB [PB Info 2022-Mar-17 12:00:56] 26.1 29.33 GB [PB Info 2022-Mar-17 12:01:06] 26.6 29.77 GB [PB Info 2022-Mar-17 12:01:16] 27.1 29.43 GB [PB Info 2022-Mar-17 12:01:26] 27.7 29.81 GB [PB Info 2022-Mar-17 12:01:36] 28.3 29.01 GB [PB Info 2022-Mar-17 12:01:46] 28.9 29.81 GB [PB Info 2022-Mar-17 12:01:56] 29.5 29.18 GB [PB Info 2022-Mar-17 12:02:06] 30.1 30.04 GB [PB Info 2022-Mar-17 12:02:16] 30.7 29.35 GB [PB Info 2022-Mar-17 12:02:26] 31.2 30.12 GB [PB Info 2022-Mar-17 12:02:36] 31.8 29.33 GB [PB Info 2022-Mar-17 12:02:46] 32.3 29.00 GB [PB Info 2022-Mar-17 12:02:56] 32.8 29.61 GB [PB Info 2022-Mar-17 12:03:06] 33.4 29.26 GB [PB Info 2022-Mar-17 12:03:16] 34.0 29.69 GB [PB Info 2022-Mar-17 12:03:26] 34.6 28.74 GB [PB Info 2022-Mar-17 12:03:36] 35.1 29.18 GB [PB Info 2022-Mar-17 12:03:46] 35.7 29.10 GB [PB Info 2022-Mar-17 12:03:56] 36.2 29.93 GB [PB Info 2022-Mar-17 12:04:06] 36.7 29.68 GB [PB Info 2022-Mar-17 12:04:16] 37.6 29.14 GB [PB Info 2022-Mar-17 12:04:26] 37.9 29.15 GB [PB Info 2022-Mar-17 12:04:36] 38.3 29.64 GB [PB Info 2022-Mar-17 12:04:46] 39.2 29.09 GB [PB Info 2022-Mar-17 12:04:56] 39.5 29.22 GB [PB Info 2022-Mar-17 12:05:06] 40.1 29.22 GB [PB Info 2022-Mar-17 12:05:16] 40.7 29.21 GB [PB Info 2022-Mar-17 12:05:26] 41.2 28.99 GB [PB Info 2022-Mar-17 12:05:36] 41.8 29.52 GB [PB Info 2022-Mar-17 12:05:46] 42.4 29.95 GB [PB Info 2022-Mar-17 12:05:56] 43.0 29.25 GB [PB Info 2022-Mar-17 12:06:06] 43.6 29.85 GB [PB Info 2022-Mar-17 12:06:16] 44.0 29.87 GB [PB Info 2022-Mar-17 12:06:26] 44.5 29.07 GB [PB Info 2022-Mar-17 12:06:36] 45.1 30.25 GB [PB Info 2022-Mar-17 12:06:46] 45.7 29.33 GB [PB Info 2022-Mar-17 12:06:56] 46.2 29.10 GB [PB Info 2022-Mar-17 12:07:06] 46.8 29.82 GB [PB Info 2022-Mar-17 12:07:16] 47.3 29.43 GB [PB Info 2022-Mar-17 12:07:26] 47.8 29.27 GB [PB Info 2022-Mar-17 12:07:36] 48.9 28.90 GB [PB Info 2022-Mar-17 12:07:46] 49.4 30.06 GB [PB Info 2022-Mar-17 12:07:56] 50.0 29.20 GB [PB Info 2022-Mar-17 12:08:06] 50.5 29.35 GB [PB Info 2022-Mar-17 12:08:16] 51.0 30.03 GB [PB Info 2022-Mar-17 12:08:26] 51.5 29.51 GB [PB Info 2022-Mar-17 12:08:36] 52.0 29.24 GB [PB Info 2022-Mar-17 12:08:46] 52.6 29.65 GB [PB Info 2022-Mar-17 12:08:56] 53.1 29.22 GB [PB Info 2022-Mar-17 12:09:06] 53.7 29.60 GB [PB Info 2022-Mar-17 12:09:16] 54.3 29.25 GB [PB Info 2022-Mar-17 12:09:26] 54.8 29.19 GB [PB Info 2022-Mar-17 12:09:36] 55.3 29.46 GB [PB Info 2022-Mar-17 12:09:46] 55.9 29.39 GB [PB Info 2022-Mar-17 12:09:56] 56.4 29.02 GB [PB Info 2022-Mar-17 12:10:06] 57.0 29.32 GB [PB Info 2022-Mar-17 12:10:16] 57.5 28.87 GB [PB Info 2022-Mar-17 12:10:26] 58.1 29.50 GB [PB Info 2022-Mar-17 12:10:36] 58.6 29.11 GB [PB Info 2022-Mar-17 12:10:46] 59.2 29.00 GB [PB Info 2022-Mar-17 12:10:56] 59.7 29.53 GB [PB Info 2022-Mar-17 12:11:06] 60.3 29.17 GB [PB Info 2022-Mar-17 12:11:16] 60.9 29.98 GB [PB Info 2022-Mar-17 12:11:26] 61.4 29.59 GB [PB Info 2022-Mar-17 12:11:36] 61.9 29.22 GB [PB Info 2022-Mar-17 12:11:46] 62.5 28.99 GB [PB Info 2022-Mar-17 12:11:56] 63.0 29.25 GB [PB Info 2022-Mar-17 12:12:06] 64.0 29.78 GB [PB Info 2022-Mar-17 12:12:16] 64.4 29.88 GB [PB Info 2022-Mar-17 12:12:26] 65.0 29.11 GB [PB Info 2022-Mar-17 12:12:36] 65.6 29.59 GB [PB Info 2022-Mar-17 12:12:46] 66.2 29.26 GB [PB Info 2022-Mar-17 12:12:56] 66.7 29.66 GB [PB Info 2022-Mar-17 12:13:06] 67.7 29.09 GB [PB Info 2022-Mar-17 12:13:16] 68.2 28.87 GB [PB Info 2022-Mar-17 12:13:26] 68.9 29.32 GB [PB Info 2022-Mar-17 12:13:36] 69.3 29.03 GB [PB Info 2022-Mar-17 12:13:46] 69.9 29.67 GB [PB Info 2022-Mar-17 12:13:56] 71.0 30.05 GB [PB Info 2022-Mar-17 12:14:06] 71.6 29.19 GB [PB Info 2022-Mar-17 12:14:16] 72.2 29.16 GB [PB Info 2022-Mar-17 12:14:26] 72.7 29.48 GB [PB Info 2022-Mar-17 12:14:36] 73.3 29.87 GB [PB Info 2022-Mar-17 12:14:46] 73.7 29.32 GB [PB Info 2022-Mar-17 12:14:56] 74.2 29.14 GB [PB Info 2022-Mar-17 12:15:06] 74.9 29.23 GB [PB Info 2022-Mar-17 12:15:16] 75.5 28.96 GB [PB Info 2022-Mar-17 12:15:26] 75.9 29.64 GB [PB Info 2022-Mar-17 12:15:36] 76.5 30.75 GB [PB Info 2022-Mar-17 12:15:46] 77.0 30.30 GB [PB Info 2022-Mar-17 12:15:56] 77.7 29.02 GB [PB Info 2022-Mar-17 12:16:06] 78.2 29.37 GB [PB Info 2022-Mar-17 12:16:16] 78.7 29.17 GB [PB Info 2022-Mar-17 12:16:26] 79.3 29.00 GB [PB Info 2022-Mar-17 12:16:36] 79.8 29.32 GB [PB Info 2022-Mar-17 12:16:46] 80.3 29.77 GB [PB Info 2022-Mar-17 12:16:56] 80.9 29.02 GB [PB Info 2022-Mar-17 12:17:06] 81.4 29.35 GB [PB Info 2022-Mar-17 12:17:16] 82.1 29.55 GB [PB Info 2022-Mar-17 12:17:26] 82.6 29.07 GB [PB Info 2022-Mar-17 12:17:36] 83.2 29.35 GB [PB Info 2022-Mar-17 12:17:46] 83.7 28.97 GB [PB Info 2022-Mar-17 12:17:56] 84.3 29.15 GB [PB Info 2022-Mar-17 12:18:06] 84.7 30.30 GB [PB Info 2022-Mar-17 12:18:16] 85.3 29.46 GB [PB Info 2022-Mar-17 12:18:26] 85.9 29.57 GB [PB Info 2022-Mar-17 12:18:36] 86.6 28.91 GB [PB Info 2022-Mar-17 12:18:46] 87.0 29.08 GB [PB Info 2022-Mar-17 12:18:56] 87.7 28.61 GB [PB Info 2022-Mar-17 12:19:06] 88.3 29.32 GB [PB Info 2022-Mar-17 12:19:16] 88.9 27.95 GB [PB Info 2022-Mar-17 12:19:26] 89.9 24.19 GB [PB Info 2022-Mar-17 12:19:36] 92.3 14.47 GB [PB Info 2022-Mar-17 12:19:46] 95.8 6.36 GB [PB Info 2022-Mar-17 12:19:56] 100.0 0.00 GB [PB Info 2022-Mar-17 12:20:06] BQSR and writing final BAM: 1769.367 seconds [PB Info 2022-Mar-17 12:20:06] ------------------------------------------------------------------------------ [PB Info 2022-Mar-17 12:20:06] || Program: Marking Duplicates, BQSR || [PB Info 2022-Mar-17 12:20:06] || Version: 3.7.0-1 || [PB Info 2022-Mar-17 12:20:06] || Start Time: Thu Mar 17 11:50:36 2022 || [PB Info 2022-Mar-17 12:20:06] || End Time: Thu Mar 17 12:20:06 2022 || [PB Info 2022-Mar-17 12:20:06] || Total Time: 29 minutes 30 seconds || [PB Info 2022-Mar-17 12:20:06] ------------------------------------------------------------------------------ [PB Info 2022-Mar-17 12:20:23] ------------------------------------------------------------------------------ [PB Info 2022-Mar-17 12:20:23] || Parabricks accelerated Genomics Pipeline || [PB Info 2022-Mar-17 12:20:23] || Version 3.7.0-1 || [PB Info 2022-Mar-17 12:20:23] || GPU-GATK4 HaplotypeCaller || [PB Info 2022-Mar-17 12:20:23] || Contact: Parabricks-Support@nvidia.com || [PB Info 2022-Mar-17 12:20:23] ------------------------------------------------------------------------------ gpg: keyblock resource '/home/ubuntu/.gnupg/pubring.kbx': Permission denied [PB Info 2022-Mar-17 12:20:50] 0 /workspace/output/output.bam/workspace/output/output.vcf [PB Info 2022-Mar-17 12:20:51] ProgressMeter - Current-Locus Elapsed-Minutes Regions-Processed Regions/Minute [PB Info 2022-Mar-17 12:21:01] chr1:10382127 0.2 58049 348294 [PB Info 2022-Mar-17 12:21:11] chr1:18287934 0.3 102856 308568 [PB Info 2022-Mar-17 12:21:21] chr1:29044610 0.5 162708 325416 [PB Info 2022-Mar-17 12:21:31] chr1:40214246 0.7 225114 337671 [PB Info 2022-Mar-17 12:21:41] chr1:52358368 0.8 290739 348886 [PB Info 2022-Mar-17 12:21:51] chr1:63374284 1.0 353894 353894 [PB Info 2022-Mar-17 12:22:01] chr1:75105596 1.2 419996 359996 [PB Info 2022-Mar-17 12:22:11] chr1:86687943 1.3 486927 365195 [PB Info 2022-Mar-17 12:22:21] chr1:98433456 1.5 552665 368443 [PB Info 2022-Mar-17 12:22:31] chr1:109670257 1.7 617655 370593 [PB Info 2022-Mar-17 12:22:41] chr1:120964702 1.8 680446 371152 [PB Info 2022-Mar-17 12:22:51] chr1:123633349 2.0 697355 348677 [PB Info 2022-Mar-17 12:23:01] chr1:124252700 2.2 702766 324353 [PB Info 2022-Mar-17 12:23:11] chr1:124771159 2.3 707327 303140 [PB Info 2022-Mar-17 12:23:21] chr1:143279760 2.5 710964 284385 [PB Info 2022-Mar-17 12:23:31] chr1:143942374 2.7 714340 267877 [PB Info 2022-Mar-17 12:23:41] chr1:146102325 2.8 722773 255096 [PB Info 2022-Mar-17 12:23:51] chr1:146227003 3.0 723386 241128 [PB Info 2022-Mar-17 12:24:01] chr1:146323162 3.2 723695 228535 [PB Info 2022-Mar-17 12:24:11] chr1:146347152 3.3 723812 217143 [PB Info 2022-Mar-17 12:24:21] chr1:146577511 3.5 724885 207110 [PB Info 2022-Mar-17 12:24:31] chr1:148046062 3.7 733155 199951 [PB Info 2022-Mar-17 12:24:41] chr1:160521122 3.8 801720 209144 [PB Info 2022-Mar-17 12:24:51] chr1:172070353 4.0 868797 217199 [PB Info 2022-Mar-17 12:25:01] chr1:184435025 4.2 937599 225023 [PB Info 2022-Mar-17 12:25:11] chr1:196866914 4.3 1008354 232697 [PB Info 2022-Mar-17 12:25:21] chr1:208694302 4.5 1072807 238401 [PB Info 2022-Mar-17 12:25:31] chr1:220415955 4.7 1139947 244274 [PB Info 2022-Mar-17 12:25:41] chr1:231258993 4.8 1203290 248956 [PB Info 2022-Mar-17 12:25:51] chr1:241319806 5.0 1262786 252557 [PB Info 2022-Mar-17 12:26:01] chr2:3743840 5.2 1321541 255782 [PB Info 2022-Mar-17 12:26:11] chr2:14500563 5.3 1384803 259650 [PB Info 2022-Mar-17 12:26:21] chr2:26399731 5.5 1450728 263768 [PB Info 2022-Mar-17 12:26:31] chr2:37290940 5.7 1513855 267150 [PB Info 2022-Mar-17 12:26:41] chr2:47351849 5.8 1573442 269732 [PB Info 2022-Mar-17 12:26:51] chr2:57705521 6.0 1634908 272484 [PB Info 2022-Mar-17 12:27:01] chr2:69393556 6.2 1698437 275422 [PB Info 2022-Mar-17 12:27:11] chr2:79867200 6.3 1758277 277622 [PB Info 2022-Mar-17 12:27:21] chr2:92087742 6.5 1817422 279603 [PB Info 2022-Mar-17 12:27:31] chr2:98404723 6.7 1850662 277599 [PB Info 2022-Mar-17 12:27:41] chr2:109089583 6.8 1909970 279507 [PB Info 2022-Mar-17 12:27:51] chr2:120152493 7.0 1970491 281498 [PB Info 2022-Mar-17 12:28:01] chr2:130588605 7.2 2030378 283308 [PB Info 2022-Mar-17 12:28:11] chr2:140836742 7.3 2088873 284846 [PB Info 2022-Mar-17 12:28:21] chr2:151982185 7.5 2152089 286945 [PB Info 2022-Mar-17 12:28:31] chr2:163329425 7.7 2215602 288991 [PB Info 2022-Mar-17 12:28:41] chr2:173900897 7.8 2276123 290568 [PB Info 2022-Mar-17 12:28:51] chr2:184929527 8.0 2338998 292374 [PB Info 2022-Mar-17 12:29:01] chr2:196243121 8.2 2403492 294305 [PB Info 2022-Mar-17 12:29:11] chr2:207811125 8.3 2466079 295929 [PB Info 2022-Mar-17 12:29:21] chr2:218697397 8.5 2527637 297369 [PB Info 2022-Mar-17 12:29:31] chr2:229051191 8.7 2586888 298487 [PB Info 2022-Mar-17 12:29:41] chr2:239001510 8.8 2644299 299354 [PB Info 2022-Mar-17 12:29:51] chr3:5951970 9.0 2699802 299978 [PB Info 2022-Mar-17 12:30:01] chr3:15686354 9.2 2755883 300641 [PB Info 2022-Mar-17 12:30:11] chr3:27019049 9.3 2818762 302010 [PB Info 2022-Mar-17 12:30:21] chr3:38020687 9.5 2880413 303201 [PB Info 2022-Mar-17 12:30:31] chr3:49478382 9.7 2942406 304386 [PB Info 2022-Mar-17 12:30:41] chr3:60091103 9.8 3002050 305293 [PB Info 2022-Mar-17 12:30:51] chr3:70175776 10.0 3062323 306232 [PB Info 2022-Mar-17 12:31:01] chr3:78423007 10.2 3109717 305873 [PB Info 2022-Mar-17 12:31:11] chr3:89092609 10.3 3172789 307044 [PB Info 2022-Mar-17 12:31:21] chr3:97291094 10.5 3213935 306089 [PB Info 2022-Mar-17 12:31:31] chr3:107999830 10.7 3275771 307103 [PB Info 2022-Mar-17 12:31:41] chr3:119265534 10.8 3340129 308319 [PB Info 2022-Mar-17 12:31:51] chr3:130037001 11.0 3400230 309111 [PB Info 2022-Mar-17 12:32:01] chr3:140803052 11.2 3460454 309891 [PB Info 2022-Mar-17 12:32:11] chr3:152327037 11.3 3523748 310918 [PB Info 2022-Mar-17 12:32:21] chr3:163732535 11.5 3586445 311864 [PB Info 2022-Mar-17 12:32:31] chr3:175790249 11.7 3650666 312914 [PB Info 2022-Mar-17 12:32:41] chr3:186911743 11.8 3710885 313595 [PB Info 2022-Mar-17 12:32:51] chr3:196559703 12.0 3767592 313966 [PB Info 2022-Mar-17 12:33:01] chr4:7276631 12.2 3817865 313797 [PB Info 2022-Mar-17 12:33:11] chr4:15652536 12.3 3868787 313685 [PB Info 2022-Mar-17 12:33:21] chr4:26913360 12.5 3931101 314488 [PB Info 2022-Mar-17 12:33:31] chr4:37516524 12.7 3992161 315170 [PB Info 2022-Mar-17 12:33:41] chr4:47783937 12.8 4052680 315793 [PB Info 2022-Mar-17 12:33:51] chr4:51311859 13.0 4068366 312951 [PB Info 2022-Mar-17 12:34:01] chr4:51652721 13.2 4069662 309088 [PB Info 2022-Mar-17 12:34:11] chr4:52771181 13.3 4075292 305646 [PB Info 2022-Mar-17 12:34:21] chr4:62582172 13.5 4132358 306100 [PB Info 2022-Mar-17 12:34:31] chr4:73516749 13.7 4195337 306975 [PB Info 2022-Mar-17 12:34:41] chr4:83884797 13.8 4255042 307593 [PB Info 2022-Mar-17 12:34:51] chr4:95529587 14.0 4318191 308442 [PB Info 2022-Mar-17 12:35:01] chr4:107462399 14.2 4383818 309445 [PB Info 2022-Mar-17 12:35:11] chr4:118238215 14.3 4446170 310197 [PB Info 2022-Mar-17 12:35:21] chr4:128961570 14.5 4508577 310936 [PB Info 2022-Mar-17 12:35:31] chr4:139732623 14.7 4571926 311722 [PB Info 2022-Mar-17 12:35:41] chr4:150465462 14.8 4632728 312318 [PB Info 2022-Mar-17 12:35:51] chr4:161467040 15.0 4694876 312991 [PB Info 2022-Mar-17 12:36:01] chr4:171191914 15.2 4753538 313420 [PB Info 2022-Mar-17 12:36:11] chr4:181151746 15.3 4813642 313933 [PB Info 2022-Mar-17 12:36:21] chr5:215921 15.5 4865312 313891 [PB Info 2022-Mar-17 12:36:31] chr5:4598285 15.7 4891375 312215 [PB Info 2022-Mar-17 12:36:41] chr5:14620587 15.8 4950686 312674 [PB Info 2022-Mar-17 12:36:51] chr5:24983912 16.0 5009526 313095 [PB Info 2022-Mar-17 12:37:01] chr5:35198398 16.2 5068659 313525 [PB Info 2022-Mar-17 12:37:11] chr5:45787013 16.3 5127808 313947 [PB Info 2022-Mar-17 12:37:21] chr5:50145510 16.5 5140865 311567 [PB Info 2022-Mar-17 12:37:31] chr5:53361312 16.7 5159232 309553 [PB Info 2022-Mar-17 12:37:41] chr5:64363185 16.8 5220917 310153 [PB Info 2022-Mar-17 12:37:51] chr5:77793589 17.0 5286668 310980 [PB Info 2022-Mar-17 12:38:01] chr5:89083121 17.2 5349066 311596 [PB Info 2022-Mar-17 12:38:11] chr5:101620355 17.3 5415261 312418 [PB Info 2022-Mar-17 12:38:21] chr5:113327757 17.5 5480446 313168 [PB Info 2022-Mar-17 12:38:31] chr5:124867142 17.7 5544928 313863 [PB Info 2022-Mar-17 12:38:41] chr5:136506945 17.8 5608015 314468 [PB Info 2022-Mar-17 12:38:51] chr5:148271705 18.0 5671345 315074 [PB Info 2022-Mar-17 12:39:01] chr5:159426971 18.2 5732579 315554 [PB Info 2022-Mar-17 12:39:11] chr5:170277789 18.3 5794275 316051 [PB Info 2022-Mar-17 12:39:21] chr5:179721518 18.5 5849867 316209 [PB Info 2022-Mar-17 12:39:31] chr6:7507195 18.7 5904287 316301 [PB Info 2022-Mar-17 12:39:41] chr6:17202937 18.8 5960870 316506 [PB Info 2022-Mar-17 12:39:51] chr6:26539196 19.0 6017084 316688 [PB Info 2022-Mar-17 12:40:01] chr6:41284756 19.2 6079625 317197 [PB Info 2022-Mar-17 12:40:11] chr6:51791895 19.3 6139545 317562 [PB Info 2022-Mar-17 12:40:21] chr6:63815796 19.5 6203205 318113 [PB Info 2022-Mar-17 12:40:31] chr6:74999914 19.7 6265819 318600 [PB Info 2022-Mar-17 12:40:41] chr6:85958376 19.8 6329369 319127 [PB Info 2022-Mar-17 12:40:51] chr6:96479901 20.0 6391154 319557 [PB Info 2022-Mar-17 12:41:01] chr6:107678346 20.2 6454823 320073 [PB Info 2022-Mar-17 12:41:11] chr6:119188583 20.3 6519519 320632 [PB Info 2022-Mar-17 12:41:21] chr6:132287742 20.5 6589237 321426 [PB Info 2022-Mar-17 12:41:31] chr6:144911707 20.7 6657805 322151 [PB Info 2022-Mar-17 12:41:41] chr6:156473037 20.8 6724179 322760 [PB Info 2022-Mar-17 12:41:51] chr6:166718378 21.0 6784239 323059 [PB Info 2022-Mar-17 12:42:01] chr7:5371132 21.2 6838426 323075 [PB Info 2022-Mar-17 12:42:11] chr7:15287828 21.3 6900257 323449 [PB Info 2022-Mar-17 12:42:21] chr7:26169549 21.5 6965298 323967 [PB Info 2022-Mar-17 12:42:31] chr7:37790272 21.7 7030605 324489 [PB Info 2022-Mar-17 12:42:41] chr7:49583795 21.8 7097511 325076 [PB Info 2022-Mar-17 12:42:51] chr7:61238388 22.0 7160077 325458 [PB Info 2022-Mar-17 12:43:01] chr7:67910254 22.2 7200608 324839 [PB Info 2022-Mar-17 12:43:11] chr7:78455867 22.3 7259790 325065 [PB Info 2022-Mar-17 12:43:21] chr7:89985567 22.5 7326404 325617 [PB Info 2022-Mar-17 12:43:31] chr7:101831240 22.7 7392323 326131 [PB Info 2022-Mar-17 12:43:41] chr7:112607940 22.8 7452204 326373 [PB Info 2022-Mar-17 12:43:51] chr7:125625424 23.0 7522486 327064 [PB Info 2022-Mar-17 12:44:01] chr7:137063772 23.2 7585906 327449 [PB Info 2022-Mar-17 12:44:11] chr7:150047891 23.3 7653877 328023 [PB Info 2022-Mar-17 12:44:21] chr7:158687939 23.5 7705221 327881 [PB Info 2022-Mar-17 12:44:31] chr8:9479907 23.7 7761975 327970 [PB Info 2022-Mar-17 12:44:41] chr8:17385578 23.8 7813758 327849 [PB Info 2022-Mar-17 12:44:51] chr8:27369311 24.0 7873806 328075 [PB Info 2022-Mar-17 12:45:01] chr8:39023815 24.2 7938849 328504 [PB Info 2022-Mar-17 12:45:11] chr8:53217553 24.3 8012398 329276 [PB Info 2022-Mar-17 12:45:21] chr8:64367827 24.5 8074728 329580 [PB Info 2022-Mar-17 12:45:31] chr8:76012759 24.7 8137550 329900 [PB Info 2022-Mar-17 12:45:41] chr8:87714955 24.8 8200673 330228 [PB Info 2022-Mar-17 12:45:51] chr8:98726176 25.0 8260231 330409 [PB Info 2022-Mar-17 12:46:01] chr8:110419058 25.2 8322649 330701 [PB Info 2022-Mar-17 12:46:11] chr8:122452773 25.3 8388381 331120 [PB Info 2022-Mar-17 12:46:21] chr8:133415862 25.5 8449046 331335 [PB Info 2022-Mar-17 12:46:31] chr8:142833454 25.7 8505261 331373 [PB Info 2022-Mar-17 12:46:41] chr9:7223707 25.8 8560659 331380 [PB Info 2022-Mar-17 12:46:51] chr9:16762877 26.0 8618849 331494 [PB Info 2022-Mar-17 12:47:01] chr9:27417432 26.2 8680944 331755 [PB Info 2022-Mar-17 12:47:11] chr9:37458938 26.3 8740573 331920 [PB Info 2022-Mar-17 12:47:21] chr9:42287917 26.5 8768703 330894 [PB Info 2022-Mar-17 12:47:31] chr9:64603189 26.7 8804845 330181 [PB Info 2022-Mar-17 12:47:41] chr9:71894164 26.8 8840898 329474 [PB Info 2022-Mar-17 12:47:51] chr9:82689558 27.0 8901700 329692 [PB Info 2022-Mar-17 12:48:01] chr9:93115178 27.2 8960162 329821 [PB Info 2022-Mar-17 12:48:11] chr9:104159819 27.3 9020837 330030 [PB Info 2022-Mar-17 12:48:21] chr9:114594910 27.5 9081343 330230 [PB Info 2022-Mar-17 12:48:31] chr9:125481314 27.7 9141361 330410 [PB Info 2022-Mar-17 12:48:41] chr9:134543975 27.8 9194849 330353 [PB Info 2022-Mar-17 12:48:51] chr10:4742187 28.0 9246337 330226 [PB Info 2022-Mar-17 12:49:01] chr10:13718356 28.2 9301640 330235 [PB Info 2022-Mar-17 12:49:11] chr10:23932799 28.3 9360554 330372 [PB Info 2022-Mar-17 12:49:21] chr10:33417525 28.5 9416309 330396 [PB Info 2022-Mar-17 12:49:31] chr10:39907080 28.7 9453718 329780 [PB Info 2022-Mar-17 12:49:41] chr10:43602940 28.8 9471510 328491 [PB Info 2022-Mar-17 12:49:51] chr10:43703956 29.0 9472162 326626 [PB Info 2022-Mar-17 12:50:01] chr10:43723196 29.2 9472314 324765 [PB Info 2022-Mar-17 12:50:11] chr10:48825594 29.3 9498873 323825 [PB Info 2022-Mar-17 12:50:21] chr10:58611969 29.5 9557470 323982 [PB Info 2022-Mar-17 12:50:31] chr10:69062176 29.7 9618053 324204 [PB Info 2022-Mar-17 12:50:41] chr10:79612709 29.8 9675674 324324 [PB Info 2022-Mar-17 12:50:51] chr10:90273463 30.0 9737248 324574 [PB Info 2022-Mar-17 12:51:01] chr10:101169429 30.2 9797822 324789 [PB Info 2022-Mar-17 12:51:11] chr10:111806104 30.3 9858331 324999 [PB Info 2022-Mar-17 12:51:21] chr10:121785513 30.5 9916495 325130 [PB Info 2022-Mar-17 12:51:31] chr10:130380180 30.7 9967686 325033 [PB Info 2022-Mar-17 12:51:41] chr11:3667093 30.8 10006766 324543 [PB Info 2022-Mar-17 12:51:51] chr11:12542347 31.0 10059960 324514 [PB Info 2022-Mar-17 12:52:01] chr11:22531159 31.2 10119100 324677 [PB Info 2022-Mar-17 12:52:11] chr11:32587089 31.3 10178124 324833 [PB Info 2022-Mar-17 12:52:21] chr11:42887892 31.5 10238886 325044 [PB Info 2022-Mar-17 12:52:31] chr11:55579130 31.7 10311853 325637 [PB Info 2022-Mar-17 12:52:41] chr11:66465554 31.8 10371580 325808 [PB Info 2022-Mar-17 12:52:51] chr11:76430198 32.0 10427296 325853 [PB Info 2022-Mar-17 12:53:01] chr11:87182355 32.2 10488996 326082 [PB Info 2022-Mar-17 12:53:11] chr11:97617371 32.3 10549253 326265 [PB Info 2022-Mar-17 12:53:21] chr11:107447944 32.5 10608758 326423 [PB Info 2022-Mar-17 12:53:31] chr11:118257577 32.7 10669609 326620 [PB Info 2022-Mar-17 12:53:41] chr11:127670363 32.8 10724709 326640 [PB Info 2022-Mar-17 12:53:51] chr12:3211183 33.0 10784386 326799 [PB Info 2022-Mar-17 12:54:01] chr12:12585306 33.2 10837163 326748 [PB Info 2022-Mar-17 12:54:11] chr12:23063971 33.3 10898711 326961 [PB Info 2022-Mar-17 12:54:21] chr12:33763157 33.5 10961362 327204 [PB Info 2022-Mar-17 12:54:31] chr12:46027176 33.7 11030792 327647 [PB Info 2022-Mar-17 12:54:41] chr12:57431925 33.8 11095122 327934 [PB Info 2022-Mar-17 12:54:51] chr12:69422384 34.0 11162797 328317 [PB Info 2022-Mar-17 12:55:01] chr12:81791969 34.2 11232318 328750 [PB Info 2022-Mar-17 12:55:11] chr12:94439888 34.3 11301898 329181 [PB Info 2022-Mar-17 12:55:21] chr12:105705582 34.5 11366339 329459 [PB Info 2022-Mar-17 12:55:31] chr12:117393312 34.7 11431229 329746 [PB Info 2022-Mar-17 12:55:41] chr12:127660695 34.8 11490967 329884 [PB Info 2022-Mar-17 12:55:51] chr13:16766401 35.0 11533094 329516 [PB Info 2022-Mar-17 12:56:01] chr13:18590303 35.2 11546668 328341 [PB Info 2022-Mar-17 12:56:11] chr13:25910126 35.3 11590799 328041 [PB Info 2022-Mar-17 12:56:21] chr13:36614281 35.5 11653076 328255 [PB Info 2022-Mar-17 12:56:31] chr13:47721430 35.7 11718634 328559 [PB Info 2022-Mar-17 12:56:41] chr13:59548657 35.8 11786281 328919 [PB Info 2022-Mar-17 12:56:51] chr13:71313462 36.0 11853373 329260 [PB Info 2022-Mar-17 12:57:01] chr13:82857510 36.2 11920524 329599 [PB Info 2022-Mar-17 12:57:11] chr13:94103796 36.3 11985927 329887 [PB Info 2022-Mar-17 12:57:21] chr13:104755103 36.5 12048399 330093 [PB Info 2022-Mar-17 12:57:31] chr14:18456411 36.7 12106885 330187 [PB Info 2022-Mar-17 12:57:41] chr14:27489587 36.8 12159763 330129 [PB Info 2022-Mar-17 12:57:51] chr14:38855935 37.0 12225538 330419 [PB Info 2022-Mar-17 12:58:01] chr14:50275017 37.2 12292760 330746 [PB Info 2022-Mar-17 12:58:11] chr14:61339160 37.3 12357110 330994 [PB Info 2022-Mar-17 12:58:21] chr14:73473478 37.5 12424245 331313 [PB Info 2022-Mar-17 12:58:31] chr14:84767772 37.7 12488390 331550 [PB Info 2022-Mar-17 12:58:41] chr14:97166152 37.8 12551155 331748 [PB Info 2022-Mar-17 12:58:51] chr15:20375959 38.0 12612448 331906 [PB Info 2022-Mar-17 12:59:01] chr15:21508504 38.2 12618621 330618 [PB Info 2022-Mar-17 12:59:11] chr15:33782195 38.3 12676638 330694 [PB Info 2022-Mar-17 12:59:21] chr15:45859085 38.5 12743468 330999 [PB Info 2022-Mar-17 12:59:31] chr15:57273545 38.7 12809246 331273 [PB Info 2022-Mar-17 12:59:41] chr15:68553600 38.8 12872297 331475 [PB Info 2022-Mar-17 12:59:51] chr15:79679868 39.0 12935522 331680 [PB Info 2022-Mar-17 13:00:01] chr15:91348797 39.2 13000287 331922 [PB Info 2022-Mar-17 13:00:11] chr15:101750291 39.3 13062655 332101 [PB Info 2022-Mar-17 13:00:21] chr16:8174344 39.5 13114241 332006 [PB Info 2022-Mar-17 13:00:31] chr16:20049546 39.7 13177834 332214 [PB Info 2022-Mar-17 13:00:41] chr16:30743871 39.8 13237940 332333 [PB Info 2022-Mar-17 13:00:51] chr16:36748798 40.0 13263795 331594 [PB Info 2022-Mar-17 13:01:01] chr16:46684775 40.2 13270003 330373 [PB Info 2022-Mar-17 13:01:11] chr16:46910322 40.3 13271162 329037 [PB Info 2022-Mar-17 13:01:21] chr16:46934375 40.5 13271270 327685 [PB Info 2022-Mar-17 13:01:31] chr16:46972627 40.7 13271473 326347 [PB Info 2022-Mar-17 13:01:41] chr16:49271874 40.8 13282391 325283 [PB Info 2022-Mar-17 13:01:51] chr16:49281519 41.0 13282441 323961 [PB Info 2022-Mar-17 13:02:01] chr16:49281519 41.2 13282441 322650 [PB Info 2022-Mar-17 13:02:11] chr16:49286241 41.3 13282469 321350 [PB Info 2022-Mar-17 13:02:21] chr16:49300612 41.5 13282555 320061 [PB Info 2022-Mar-17 13:02:31] chr16:49305597 41.7 13282588 318782 [PB Info 2022-Mar-17 13:02:41] chr16:49305597 41.8 13282588 317512 [PB Info 2022-Mar-17 13:02:51] chr16:49847853 42.0 13285657 316325 [PB Info 2022-Mar-17 13:03:01] chr16:60897485 42.2 13350103 316603 [PB Info 2022-Mar-17 13:03:11] chr16:73516668 42.3 13417814 316956 [PB Info 2022-Mar-17 13:03:21] chr16:82809600 42.5 13475844 317078 [PB Info 2022-Mar-17 13:03:31] chr17:1219100 42.7 13529771 317104 [PB Info 2022-Mar-17 13:03:41] chr17:10886230 42.8 13586275 317189 [PB Info 2022-Mar-17 13:03:51] chr17:21451008 43.0 13647641 317387 [PB Info 2022-Mar-17 13:04:01] chr17:26812733 43.2 13669766 316674 [PB Info 2022-Mar-17 13:04:11] chr17:27964615 43.3 13676040 315600 [PB Info 2022-Mar-17 13:04:21] chr17:29073486 43.5 13681161 314509 [PB Info 2022-Mar-17 13:04:31] chr17:44327804 43.7 13753028 314954 [PB Info 2022-Mar-17 13:04:41] chr17:56803174 43.8 13819252 315268 [PB Info 2022-Mar-17 13:04:51] chr17:68534276 44.0 13884249 315551 [PB Info 2022-Mar-17 13:05:01] chr17:78854244 44.2 13942716 315684 [PB Info 2022-Mar-17 13:05:11] chr18:1603156 44.3 13978267 315299 [PB Info 2022-Mar-17 13:05:21] chr18:1804656 44.5 13979567 314147 [PB Info 2022-Mar-17 13:05:31] chr18:12220779 44.7 14041569 314363 [PB Info 2022-Mar-17 13:05:41] chr18:26519978 44.8 14115827 314851 [PB Info 2022-Mar-17 13:05:51] chr18:39162979 45.0 14185244 315227 [PB Info 2022-Mar-17 13:06:01] chr18:51239856 45.2 14251821 315538 [PB Info 2022-Mar-17 13:06:11] chr18:62313544 45.3 14315968 315793 [PB Info 2022-Mar-17 13:06:21] chr18:73031981 45.5 14380180 316047 [PB Info 2022-Mar-17 13:06:31] chr19:2683004 45.7 14438656 316174 [PB Info 2022-Mar-17 13:06:41] chr19:11486329 45.8 14491365 316175 [PB Info 2022-Mar-17 13:06:51] chr19:21350397 46.0 14547456 316249 [PB Info 2022-Mar-17 13:07:01] chr19:32980794 46.2 14598283 316208 [PB Info 2022-Mar-17 13:07:11] chr19:43391781 46.3 14654095 316275 [PB Info 2022-Mar-17 13:07:21] chr19:52838156 46.5 14709615 316335 [PB Info 2022-Mar-17 13:07:31] chr20:4823823 46.7 14768356 316464 [PB Info 2022-Mar-17 13:07:41] chr20:16247950 46.8 14834210 316744 [PB Info 2022-Mar-17 13:07:51] chr20:28756652 47.0 14899613 317013 [PB Info 2022-Mar-17 13:08:01] chr20:29572773 47.2 14904541 315997 [PB Info 2022-Mar-17 13:08:11] chr20:30206132 47.3 14908646 314971 [PB Info 2022-Mar-17 13:08:21] chr20:32500582 47.5 14920056 314106 [PB Info 2022-Mar-17 13:08:31] chr20:33743831 47.7 14926723 313148 [PB Info 2022-Mar-17 13:08:41] chr20:45777304 47.8 14992013 313421 [PB Info 2022-Mar-17 13:08:51] chr20:55958214 48.0 15051120 313565 [PB Info 2022-Mar-17 13:09:01] chr21:7967980 48.2 15103716 313571 [PB Info 2022-Mar-17 13:09:11] chr21:9614244 48.3 15110244 312625 [PB Info 2022-Mar-17 13:09:21] chr21:9767917 48.5 15111477 311576 [PB Info 2022-Mar-17 13:09:31] chr21:10084710 48.7 15114225 310566 [PB Info 2022-Mar-17 13:09:41] chr21:13036766 48.8 15119855 309621 [PB Info 2022-Mar-17 13:09:51] chr21:13526399 49.0 15123049 308633 [PB Info 2022-Mar-17 13:10:01] chr21:18729553 49.2 15152087 308178 [PB Info 2022-Mar-17 13:10:11] chr21:29020543 49.3 15213495 308381 [PB Info 2022-Mar-17 13:10:21] chr21:38827199 49.5 15268597 308456 [PB Info 2022-Mar-17 13:10:31] chr22:11059140 49.7 15316641 308388 [PB Info 2022-Mar-17 13:10:41] chr22:12191897 49.8 15322213 307469 [PB Info 2022-Mar-17 13:10:51] chr22:12575963 50.0 15324553 306491 [PB Info 2022-Mar-17 13:11:01] chr22:16305531 50.2 15333096 305643 [PB Info 2022-Mar-17 13:11:11] chr22:24052514 50.3 15374759 305458 [PB Info 2022-Mar-17 13:11:21] chr22:33657597 50.5 15429259 305529 [PB Info 2022-Mar-17 13:11:31] chr22:43852759 50.7 15484813 305621 [PB Info 2022-Mar-17 13:11:41] chrX:1060653 50.8 15532348 305554 [PB Info 2022-Mar-17 13:11:51] chrX:10089394 51.0 15582615 305541 [PB Info 2022-Mar-17 13:12:01] chrX:23346902 51.2 15647106 305806 [PB Info 2022-Mar-17 13:12:11] chrX:35933550 51.3 15712720 306091 [PB Info 2022-Mar-17 13:12:21] chrX:49281549 51.5 15779155 306391 [PB Info 2022-Mar-17 13:12:31] chrX:68097568 51.7 15859196 306952 [PB Info 2022-Mar-17 13:12:41] chrX:81311880 51.8 15927847 307289 [PB Info 2022-Mar-17 13:12:51] chrX:94074940 52.0 15996418 307623 [PB Info 2022-Mar-17 13:13:01] chrX:108710230 52.2 16067782 308008 [PB Info 2022-Mar-17 13:13:11] chrX:122500795 52.3 16135918 308329 [PB Info 2022-Mar-17 13:13:21] chrX:136223991 52.5 16203925 308646 [PB Info 2022-Mar-17 13:13:31] chrX:148574191 52.7 16269345 308911 [PB Info 2022-Mar-17 13:13:41] chrY:10843072 52.8 16331951 309122 [PB Info 2022-Mar-17 13:13:51] chr1_KI270706v1_random:67119 53.0 16366913 308809 [PB Info 2022-Mar-17 13:14:01] chr1_KI270713v1_random:9471 53.2 16370898 307916 [PB Info 2022-Mar-17 13:14:11] chr2_KI270715v1_random:100725 53.3 16372011 306975 [PB Info 2022-Mar-17 13:14:21] chr4_GL000008v2_random:110244 53.5 16374855 306072 [PB Info 2022-Mar-17 13:14:31] chr9_KI270719v1_random:91172 53.7 16377194 305165 [PB Info 2022-Mar-17 13:14:41] chr14_KI270722v1_random:43114 53.8 16382284 304314 [PB Info 2022-Mar-17 13:14:51] chr14_KI270724v1_random:19122 54.0 16385468 303434 [PB Info 2022-Mar-17 13:15:01] chr14_KI270725v1_random:105554 54.2 16386248 302515 [PB Info 2022-Mar-17 13:15:11] chr17_KI270729v1_random:86343 54.3 16393194 301715 [PB Info 2022-Mar-17 13:15:21] chr22_KI270734v1_random:18989 54.5 16397496 300871 [PB Info 2022-Mar-17 13:15:31] chr22_KI270734v1_random:100616 54.7 16397899 299961 [PB Info 2022-Mar-17 13:15:41] chrUn_KI270425v1:1612 54.8 16402020 299124 [PB Info 2022-Mar-17 13:15:51] chrUn_KI270442v1:14333 55.0 16402111 298220 [PB Info 2022-Mar-17 13:16:01] chrUn_KI270442v1:182332 55.2 16403373 297342 [PB Info 2022-Mar-17 13:16:11] chrUn_KI270512v1:9517 55.3 16406385 296500 [PB Info 2022-Mar-17 13:16:21] chrUn_GL000195v1:139084 55.5 16410506 295684 [PB Info 2022-Mar-17 13:16:31] chrUn_GL000195v1:153531 55.7 16410618 294801 [PB Info 2022-Mar-17 13:16:41] chrUn_GL000219v1:67175 55.8 16411192 293931 [PB Info 2022-Mar-17 13:16:51] chrUn_GL000219v1:177529 56.0 16412172 293074 [PB Info 2022-Mar-17 13:17:01] chrUn_GL000219v1:177529 56.2 16412172 292204 [PB Info 2022-Mar-17 13:17:11] chrUn_GL000220v1:23940 56.3 16412344 291343 [PB Info 2022-Mar-17 13:17:21] chrUn_GL000224v1:177466 56.5 16414147 290515 [PB Info 2022-Mar-17 13:17:31] chrUn_KI270746v1:62353 56.7 16418636 289740 [PB Info 2022-Mar-17 13:17:41] chrUn_KI270749v1:86190 56.8 16420880 288930 [PB Info 2022-Mar-17 13:17:51] chrUn_KI270754v1:19128 57.0 16423682 288134 [PB Info 2022-Mar-17 13:18:01] chrUn_KI270755v1:4801 57.2 16423859 287297 [PB Info 2022-Mar-17 13:18:11] chrUn_GL000218v1:23951 57.3 16428126 286537 [PB Info 2022-Mar-17 13:18:21] chr1_KI270766v1_alt:19167 57.5 16429773 285735 [PB Info 2022-Mar-17 13:18:31] chr3_KI270783v1_alt:42961 57.7 16435123 285002 [PB Info 2022-Mar-17 13:18:41] chr6_GL000254v2_alt:595046 57.8 16554002 286236 [PB Info 2022-Mar-17 13:18:51] chrUn_KN707896v1_decoy:28709 58.0 16575402 285782 [PB Info 2022-Mar-17 13:19:01] chrUn_KN707957v1_decoy:9599 58.2 16576362 284980 [PB Info 2022-Mar-17 13:19:11] chrUn_KN707958v1_decoy:2424 58.3 16576397 284166 [PB Info 2022-Mar-17 13:19:21] chrUn_KN707963v1_decoy:4610 58.5 16576468 283358 [PB Info 2022-Mar-17 13:19:31] chrUn_JTFH01000010v1_decoy:4681 58.7 16578303 282584 [PB Info 2022-Mar-17 13:19:41] chrUn_JTFH01000023v1_decoy:7015 58.8 16578720 281791 [PB Info 2022-Mar-17 13:19:51] chrUn_JTFH01000096v1_decoy:3557 59.0 16579882 281014 [PB Info 2022-Mar-17 13:20:01] chrUn_JTFH01000097v1_decoy:3569 59.2 16579900 280223 [PB Info 2022-Mar-17 13:20:11] chrUn_JTFH01000098v1_decoy:3534 59.3 16579930 279437 [PB Info 2022-Mar-17 13:20:21] chrUn_JTFH01000098v1_decoy:3534 59.5 16579930 278654 [PB Info 2022-Mar-17 13:20:31] chrUn_JTFH01000101v1_decoy:3267 59.7 16579964 277876 [PB Info 2022-Mar-17 13:20:41] chrUn_JTFH01000102v1_decoy:3490 59.8 16579985 277102 [PB Info 2022-Mar-17 13:20:51] chrUn_JTFH01000102v1_decoy:3490 60.0 16579985 276333 [PB Info 2022-Mar-17 13:21:01] chrUn_JTFH01000108v1_decoy:3324 60.2 16580082 275569 [PB Info 2022-Mar-17 13:21:11] chrUn_JTFH01000112v1_decoy:3206 60.3 16580155 274809 [PB Info 2022-Mar-17 13:21:21] chrUn_JTFH01000112v1_decoy:3206 60.5 16580155 274052 [PB Info 2022-Mar-17 13:21:31] chrUn_JTFH01000113v1_decoy:3201 60.7 16580177 273299 [PB Info 2022-Mar-17 13:21:41] chrUn_JTFH01000114v1_decoy:3179 60.8 16580212 272551 [PB Info 2022-Mar-17 13:21:51] chrUn_JTFH01000202v1_decoy:2578 61.0 16581456 271827 [PB Info 2022-Mar-17 13:22:01] chrUn_JTFH01000299v1_decoy:2099 61.2 16582442 271102 [PB Info 2022-Mar-17 13:22:11] chrUn_JTFH01000891v1_decoy:901 61.3 16586395 270430 [PB Info 2022-Mar-17 13:22:21] chrUn_JTFH01001345v1_decoy:2000 61.5 16590498 269764 [PB Info 2022-Mar-17 13:22:31] chrUn_JTFH01001851v1_decoy:3102 61.7 16596169 269127 [PB Info 2022-Mar-17 13:22:41] HLA-DRB1*15:02:01:10276 61.8 16598422 268438 [PB Info 2022-Mar-17 13:22:52] Total time taken: 3722.013167 [PB Info 2022-Mar-17 13:22:52] ------------------------------------------------------------------------------ [PB Info 2022-Mar-17 13:22:52] || Program: GPU-GATK4 HaplotypeCaller || [PB Info 2022-Mar-17 13:22:52] || Version: 3.7.0-1 || [PB Info 2022-Mar-17 13:22:52] || Start Time: Thu Mar 17 12:20:23 2022 || [PB Info 2022-Mar-17 13:22:52] || End Time: Thu Mar 17 13:22:52 2022 || [PB Info 2022-Mar-17 13:22:52] || Total Time: 62 minutes 29 seconds || [PB Info 2022-Mar-17 13:22:52] ------------------------------------------------------------------------------ exit code: Done! Thu Mar 17 13:22:53 UTC 2022 end_time: 1647523373 Total time: 6h 33m 31s [1]+ Done sh germline.sh 2>&1 | tee germline.sh.log ``` - monitor: program1 [![](https://i.imgur.com/tYIu9Yi.png)](https://i.imgur.com/tYIu9Yi.png) - CPU 使用 11/16 <br> <hr> <br> ## 執行評估 > **g4dn.4xlarge (T4 + 16vCPU + 64GB)** > - A instance: 3000IOPS, 125MiB (理想) (預設值) > - B instance: 14600IOPS, 571MiB (理想) - meminfo - MemTotal: 62.03 Gib - MemAvailable: 60.89 Gib - parms - `--memory-limit`: ml - `--num-cpu-threads`: nct - P: Program - P1: GPU-BWA mem, Sorting Phase-I - P2: Sorting Phase-II - P3: Marking Dmuplicates, BQSR - P4: GPU-GATK4 HaplotypeCaller | # | ml | nct | P1 | P2 | P3 | P4 | Total| |---|----|-----|---:|---:|---:|---:|-----:| | **A.1** | - | - | 4h55m30s | 5m40s | 29m30s | 62m29s | 6h33m31s | | **A.2** | - | - | 4h55m45s | 5m41s | 29m46s | 62m48s | 6h34m08s | || | **B.1** | - | - | 5h01m28s | 3m31s | 14m31s | 65m09s | 6h24m48s | | **B.2** | 62 | 16 | 4h16m12s | 3m31s | <span style="color: red;">killed<br>(OOM)</span> | | ~~4h20m57s~~ | | **B.3** | - | 16 | 4h17m30s | 3m30 | 14m21s | 63m30s | 5h39m00s | | **B.4** | 60 | 16 | 4h19m05s | 3m40s | <span style="color: red;">killed<br>(OOM)</span> | | ~~4h24m17s~~ | | **B.5** | 50 | 16 | 4h20m06s | 3m40s | 15m11s | 65m19s | 5h44m25s | | **B.6** | 40 | 16 | 4h21m20s| 3m41s | 15m21s| 63m49s | 5h44m20s | | **B.7** | 50 | 8 | 4h26m08s | 3m30s | 14m30s | 63m30s | 5h47m48s | | **B.8** | - | 8 | 4h23m55s | 3m40s | 15m21s | 65m40s | 5h48m46s | | **B.9** | - | 32 | 4h38m37s| 3m40s | 15m22s | 65m50s | 6h03m37s | | **B.10** | - | - | 5h00m58s | 3m31s | 14m31s | 64m10s | 6h23m18s | - **B.1** 和 **B.10** 是兩個相同參數，在不同時間點跑得結果，看起來沒有差異