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/79/3bc4bf291befd7ebfae17b0290fa46/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/7e9a8a006beae9b40e521eef1ddc92/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.md.bam 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/ac/7e9a8a006beae9b40e521eef1ddc92/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/3bc4bf291befd7ebfae17b0290fa46/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed ==> STAGING COMPLETE (8 inputs) cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.md.bam --algo HsMetricAlgo --targets_list targets/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed --baits_list baits/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed 1029_BICJ-T1-TDNA-1_A23MHWWLT4_1_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr1:189000001, elapsed 3.6s, est remaining 68.8s, peak mem 2247MB, user 64.5s, sys 1.3s, output queue size 42 progress 10% @chr2:94000001, elapsed 8.1s, est remaining 73.1s, peak mem 4051MB, user 209.8s, sys 3.3s, output queue size 172 progress 15% @chr2:224000001, elapsed 11.0s, est remaining 62.5s, peak mem 4282MB, user 312.4s, sys 4.9s, output queue size 328 progress 20% @chr3:161000001, elapsed 13.5s, est remaining 54.2s, peak mem 4282MB, user 390.5s, sys 5.5s, output queue size 489 progress 25% @chr4:136000001, elapsed 15.6s, est remaining 46.9s, peak mem 4321MB, user 451.3s, sys 6.0s, output queue size 650 progress 30% @chr5:107000001, elapsed 17.1s, est remaining 39.9s, peak mem 4321MB, user 509.8s, sys 6.5s, output queue size 464 progress 35% @chr6:92000001, elapsed 20.4s, est remaining 37.9s, peak mem 4802MB, user 593.6s, sys 7.1s, output queue size 106 progress 40% @chr7:45000001, elapsed 23.4s, est remaining 35.1s, peak mem 5323MB, user 683.8s, sys 7.8s, output queue size 197 progress 45% @chr8:54000001, elapsed 26.7s, est remaining 32.6s, peak mem 5530MB, user 775.9s, sys 8.5s, output queue size 357 progress 50% @chr9:86000001, elapsed 30.0s, est remaining 30.0s, peak mem 5792MB, user 892.7s, sys 9.6s, output queue size 187 progress 55% @chr10:109000001, elapsed 34.0s, est remaining 27.8s, peak mem 6182MB, user 1011.7s, sys 10.4s, output queue size 236 progress 60% @chr11:1000001, elapsed 37.0s, est remaining 24.6s, peak mem 6182MB, user 1096.4s, sys 11.1s, output queue size 312 progress 65% @chr13:23000001, elapsed 40.3s, est remaining 21.7s, peak mem 6420MB, user 1198.8s, sys 11.8s, output queue size 474 progress 70% @chr14:83000001, elapsed 42.7s, est remaining 18.3s, peak mem 6420MB, user 1288.1s, sys 12.5s, output queue size 261 progress 75% @chr16:42000001, elapsed 46.1s, est remaining 15.4s, peak mem 6420MB, user 1385.7s, sys 13.1s, output queue size 118 progress 80% @chr17:41000001, elapsed 50.8s, est remaining 12.7s, peak mem 6420MB, user 1518.8s, sys 14.0s, output queue size 189 progress 85% @chr20:3000001, elapsed 55.6s, est remaining 9.8s, peak mem 6547MB, user 1672.5s, sys 15.0s, output queue size 351 progress 90% @chr22:39000001, elapsed 58.7s, est remaining 6.5s, peak mem 6547MB, user 1782.1s, sys 15.8s, output queue size 78 progress 95% @chrY:52000001, elapsed 60.9s, est remaining 3.2s, peak mem 6547MB, user 1845.9s, sys 16.2s, output queue size 240 progress 100% @chr22:23000001, elapsed 65.6s, est remaining 0.0s, peak mem 6547MB, user 1899.7s, sys 16.5s, output queue size 3635 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: HsMetricAlgo license: sentieon:Metrics=31 input file size: 49280866937 reads: 991312774 contig: 3367 intervals 3217346917 bases advance: 3219322 calls 801.496 user 14.188 sys 815.458 real done: 1 calls 0.269 user 0.030 sys 0.299 real exec_no_coor: 1 calls 0.015 user 0.000 sys 0.022 real execute: 1 calls 0.006 user 0.003 sys 65.623 real idle: 188 calls 0.135 user 0.001 sys 154.667 real init: 1 calls 0.000 user 0.000 sys 0.000 real overall: 6865727488 mem 1901.469 user 16.916 sys 67.454 real