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/3d/3c1aafdc825622ffd7b9485b92b64d/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
  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/8c/fd9d16d5f12b5a7d5c9a20f5f532db/659_bR4-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/fd9d16d5f12b5a7d5c9a20f5f532db/659_bR4-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/3c1aafdc825622ffd7b9485b92b64d/.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
==> STAGING COMPLETE (8 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 659_bR4-T1-TDNA-1_A23MHWWLT4_1.md.bam --algo HsMetricAlgo --targets_list targets/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed --baits_list baits/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed 659_bR4-T1-TDNA-1_A23MHWWLT4_1_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:181000001, elapsed 5.9s, est remaining 111.4s, peak mem 4881MB, user 136.4s, sys 4.6s, output queue size 145
progress 10% @chr1:205000001, elapsed 11.4s, est remaining 102.9s, peak mem 6754MB, user 301.2s, sys 8.0s, output queue size 117
progress 15% @chr2:201000001, elapsed 16.9s, est remaining 95.7s, peak mem 10347MB, user 462.5s, sys 13.6s, output queue size 203
progress 20% @chr3:178000001, elapsed 21.2s, est remaining 84.8s, peak mem 10726MB, user 596.6s, sys 19.0s, output queue size 218
progress 25% @chr4:103000001, elapsed 24.9s, est remaining 74.8s, peak mem 10735MB, user 717.2s, sys 19.9s, output queue size 302
progress 30% @chr5:75000001, elapsed 28.2s, est remaining 65.8s, peak mem 11072MB, user 818.8s, sys 20.6s, output queue size 464
progress 35% @chr6:86000001, elapsed 32.5s, est remaining 60.3s, peak mem 11311MB, user 932.8s, sys 21.6s, output queue size 625
progress 40% @chr7:66000001, elapsed 37.2s, est remaining 55.8s, peak mem 11382MB, user 1066.4s, sys 22.8s, output queue size 786
progress 45% @chr7:100000001, elapsed 43.4s, est remaining 53.0s, peak mem 11671MB, user 1234.2s, sys 23.9s, output queue size 948
progress 50% @chr9:39000001, elapsed 48.4s, est remaining 48.4s, peak mem 12061MB, user 1389.5s, sys 25.2s, output queue size 366
progress 55% @chr10:118000001, elapsed 54.0s, est remaining 44.2s, peak mem 12190MB, user 1563.9s, sys 26.4s, output queue size 527
progress 60% @chr11:134000001, elapsed 59.3s, est remaining 39.6s, peak mem 12190MB, user 1731.4s, sys 27.5s, output queue size 689
progress 65% @chr13:36000001, elapsed 65.7s, est remaining 35.4s, peak mem 12404MB, user 1915.8s, sys 28.9s, output queue size 672
progress 70% @chr14:35000001, elapsed 69.3s, est remaining 29.7s, peak mem 12519MB, user 2013.8s, sys 29.6s, output queue size 833
progress 75% @chr16:42000001, elapsed 75.1s, est remaining 25.0s, peak mem 12652MB, user 2196.1s, sys 30.9s, output queue size 995
progress 80% @chr18:9000001, elapsed 83.7s, est remaining 20.9s, peak mem 12770MB, user 2446.0s, sys 32.2s, output queue size 623
progress 85% @chr20:25000001, elapsed 91.9s, est remaining 16.2s, peak mem 12770MB, user 2705.1s, sys 33.9s, output queue size 785
progress 90% @chr22:39000001, elapsed 96.6s, est remaining 10.7s, peak mem 13163MB, user 2891.1s, sys 35.0s, output queue size 513
progress 95% @chrY:55000001, elapsed 99.5s, est remaining 5.2s, peak mem 13163MB, user 3001.2s, sys 35.7s, output queue size 240
progress 100% @chr22:23000001, elapsed 108.4s, est remaining 0.0s, peak mem 13163MB, user 3111.6s, sys 36.5s, 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: 83203675103
reads: 1632923217
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1306.317 user 31.646 sys 1339.702 real
done: 1 calls 0.293 user 0.057 sys 0.356 real
exec_no_coor: 1 calls 0.000 user 0.011 sys 0.019 real
execute: 1 calls 0.003 user 0.002 sys 108.446 real
idle: 277 calls 0.130 user 0.001 sys 246.310 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 13803126784 mem 3113.692 user 37.061 sys 110.287 real