Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/8a67a4930c75ff0573fec03e4ea2c8/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/efd16529d13104243b107dd6dcea07/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/8a67a4930c75ff0573fec03e4ea2c8/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/efd16529d13104243b107dd6dcea07/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam ==> STAGING COMPLETE (6 inputs) cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.score This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr1:181000001, elapsed 3.3s, est remaining 63.6s, peak mem 3680MB, user 76.1s, sys 3.4s, output queue size 150 progress 10% @chr2:70000001, elapsed 6.7s, est remaining 59.9s, peak mem 5410MB, user 173.1s, sys 6.1s, output queue size 117 progress 15% @chr3:11000001, elapsed 11.0s, est remaining 62.3s, peak mem 8754MB, user 299.4s, sys 13.9s, output queue size 122 progress 20% @chr3:167000001, elapsed 13.6s, est remaining 54.2s, peak mem 8841MB, user 377.9s, sys 15.4s, output queue size 283 progress 25% @chr4:132000001, elapsed 15.8s, est remaining 47.4s, peak mem 8877MB, user 446.5s, sys 16.4s, output queue size 444 progress 30% @chr5:94000001, elapsed 17.6s, est remaining 41.0s, peak mem 9140MB, user 498.4s, sys 17.0s, output queue size 606 progress 35% @chr6:70000001, elapsed 20.6s, est remaining 38.3s, peak mem 10034MB, user 568.6s, sys 18.1s, output queue size 767 progress 40% @chr7:48000001, elapsed 24.5s, est remaining 36.7s, peak mem 11379MB, user 672.6s, sys 19.7s, output queue size 928 progress 45% @chr8:54000001, elapsed 29.8s, est remaining 36.4s, peak mem 12159MB, user 814.5s, sys 21.2s, output queue size 1090 progress 50% @chr9:87000001, elapsed 33.4s, est remaining 33.4s, peak mem 12790MB, user 912.3s, sys 22.6s, output queue size 1252 progress 55% @chr10:43000001, elapsed 36.9s, est remaining 30.2s, peak mem 15280MB, user 1052.4s, sys 25.1s, output queue size 668 progress 60% @chr11:134000001, elapsed 40.9s, est remaining 27.3s, peak mem 17654MB, user 1162.3s, sys 26.1s, output queue size 830 progress 65% @chr13:30000001, elapsed 44.8s, est remaining 24.1s, peak mem 19164MB, user 1264.1s, sys 27.3s, output queue size 992 progress 70% @chr14:84000001, elapsed 48.0s, est remaining 20.6s, peak mem 19853MB, user 1384.8s, sys 28.6s, output queue size 970 progress 75% @chr16:42000001, elapsed 52.3s, est remaining 17.4s, peak mem 22369MB, user 1492.0s, sys 29.9s, output queue size 1132 progress 80% @chr17:31000001, elapsed 57.9s, est remaining 14.5s, peak mem 23022MB, user 1675.4s, sys 31.4s, output queue size 1294 progress 85% @chr19:52000001, elapsed 63.0s, est remaining 11.1s, peak mem 23069MB, user 1835.0s, sys 32.3s, output queue size 1456 progress 90% @chrX:30000001, elapsed 66.3s, est remaining 7.4s, peak mem 23069MB, user 1934.8s, sys 33.2s, output queue size 1618 progress 95% @chrY:18000001, elapsed 68.4s, est remaining 3.6s, peak mem 23069MB, user 1999.3s, sys 33.7s, output queue size 1780 progress 100% @chr7:55000001, elapsed 598.3s, est remaining 0.0s, peak mem 34032MB, user 2606.3s, sys 74.4s, output queue size 5204 sw version: sentieon-genomics-202308.03 os version: Linux 6.12.88 cpu vendor: GenuineIntel signature: 000a06d1 features: 1f8bfbff fffab20b extended: f1bf27eb 1b407f7e amd bits: 2c100800 00000121 brand: Intel(R) Xeon(R) 6975P-C threads: 31 max 192 algo: LocusCollector license: sentieon:Dedup=31 input file size: 70449436001 reads: 1527741288 contig: 3367 intervals 3217346917 bases LocusCollector::merge: 1 calls 0.808 user 0.222 sys 1.088 real VcfLineRecordHelper::sort: 37 calls 1.849 user 0.129 sys 1.975 real advance: 3219322 calls 1276.692 user 40.947 sys 1318.083 real calc: 3219322 calls 525.983 user 13.995 sys 543.971 real done: 1 calls 0.808 user 0.222 sys 1.088 real execute: 1 calls 0.003 user 0.003 sys 598.398 real fetch: 3219322 calls 687.089 user 14.771 sys 699.672 real idle: 16338 calls 4.612 user 0.060 sys 15889.819 real init: 1 calls 0.000 user 0.000 sys 0.000 real overall: 35685765120 mem 2652.635 user 75.962 sys 601.204 real cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.metrics 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.bam This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr1:174000001, elapsed 21.4s, est remaining 407.3s, peak mem 4837MB, user 526.4s, sys 7.1s, output queue size 146 progress 10% @chr2:92000001, elapsed 40.1s, est remaining 361.3s, peak mem 7544MB, user 1141.1s, sys 12.4s, output queue size 48 progress 15% @chr2:237000001, elapsed 67.5s, est remaining 382.3s, peak mem 10247MB, user 1903.8s, sys 17.4s, output queue size 122 progress 20% @chr3:155000001, elapsed 84.6s, est remaining 338.6s, peak mem 10288MB, user 2452.6s, sys 20.9s, output queue size 283 progress 25% @chr4:113000001, elapsed 100.1s, est remaining 300.2s, peak mem 10288MB, user 2906.7s, sys 23.3s, output queue size 444 progress 30% @chr5:83000001, elapsed 112.2s, est remaining 261.8s, peak mem 10333MB, user 3290.6s, sys 25.6s, output queue size 606 progress 35% @chr6:39000001, elapsed 133.0s, est remaining 247.0s, peak mem 10984MB, user 3817.7s, sys 28.8s, output queue size 767 progress 40% @chr7:56000001, elapsed 158.5s, est remaining 237.8s, peak mem 12466MB, user 4458.1s, sys 32.5s, output queue size 928 progress 45% @chr8:78000001, elapsed 189.7s, est remaining 231.9s, peak mem 13498MB, user 5513.0s, sys 39.1s, output queue size 345 progress 50% @chr9:88000001, elapsed 212.3s, est remaining 212.3s, peak mem 18912MB, user 6108.8s, sys 43.0s, output queue size 507 progress 55% @chr10:103000001, elapsed 234.6s, est remaining 192.0s, peak mem 20081MB, user 6786.0s, sys 47.7s, output queue size 668 progress 60% @chr11:130000001, elapsed 261.3s, est remaining 174.2s, peak mem 21694MB, user 7515.1s, sys 51.4s, output queue size 830 progress 65% @chr12:114000001, elapsed 286.2s, est remaining 154.1s, peak mem 22762MB, user 8390.0s, sys 55.9s, output queue size 809 progress 70% @chr14:84000001, elapsed 307.3s, est remaining 131.7s, peak mem 24291MB, user 8966.9s, sys 58.6s, output queue size 970 progress 75% @chr16:42000001, elapsed 333.4s, est remaining 111.1s, peak mem 24810MB, user 9818.3s, sys 62.5s, output queue size 1132 progress 80% @chr18:15000001, elapsed 367.5s, est remaining 91.9s, peak mem 24979MB, user 10815.7s, sys 66.9s, output queue size 1294 progress 85% @chr19:45000001, elapsed 399.4s, est remaining 70.5s, peak mem 25005MB, user 11763.5s, sys 70.8s, output queue size 1456 progress 90% @chrX:31000001, elapsed 420.8s, est remaining 46.8s, peak mem 25005MB, user 12432.4s, sys 73.9s, output queue size 1618 progress 95% @chrY:55000001, elapsed 434.7s, est remaining 22.9s, peak mem 25005MB, user 12919.8s, sys 75.7s, output queue size 1780 progress 100% @chr7:55000001, elapsed 3607.6s, est remaining 0.0s, peak mem 37905MB, user 16512.4s, sys 228.6s, output queue size 5204 library 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1: chimeric_paired 22225154 duped 1024489924 duped_chimeric_paired 4897662 duped_paired 1024483347 duped_unpaired 6577 optical_dup 87475907 paired 1513865132 reads 1527728830 secondary_supplementary 13849282 unmapped 19666 unpaired 7208 optical dup clusters 43661562, maxdup 95, total optical dup pairs 87475907 sw version: sentieon-genomics-202308.03 os version: Linux 6.12.88 cpu vendor: GenuineIntel signature: 000a06d1 features: 1f8bfbff fffab20b extended: f1bf27eb 1b407f7e amd bits: 2c100800 00000121 brand: Intel(R) Xeon(R) 6975P-C threads: 31 max 192 algo: Dedup license: sentieon:Dedup=31 input file size: 70449436001 reads: 1527741288 contig: 3367 intervals 3217346917 bases MateInfoByVcf::buildInfoMap: 2701620 calls 9.980 user 0.444 sys 10.926 real MateInfoByVcf::load: 2701620 calls 2092.421 user 13.011 sys 2007.831 real MateInfoByVcf::parse_events: 2701620 calls 1991.781 user 11.249 sys 1945.311 real advance: 3219322 calls 1211.009 user 35.630 sys 1345.557 real calc: 3219322 calls 12021.964 user 148.069 sys 12255.991 real done: 1 calls 0.049 user 0.017 sys 0.073 real exec_no_coor: 1 calls 0.087 user 0.018 sys 0.118 real execute: 1 calls 0.004 user 0.006 sys 3615.155 real fetch: 3219323 calls 845.830 user 21.315 sys 853.926 real find_pairEnds: 2701620 calls 1096.069 user 18.021 sys 1136.352 real idle: 1154849 calls 539.678 user 9.340 sys 94642.652 real init: 1 calls 0.000 user 0.000 sys 0.006 real markDup: 2701620 calls 4402.540 user 88.252 sys 4599.638 real vcfadvance: 2701620 calls 5.786 user 0.753 sys 5.768 real write: 3219323 calls 7516.164 user 57.896 sys 7544.113 real overall: 39746482176 mem 17153.529 user 262.340 sys 3617.383 real