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/fb/fef43324c03a77171b95d3996db85e/.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/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/ac/7e9a8a006beae9b40e521eef1ddc92/1029_BICJ-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/fef43324c03a77171b95d3996db85e/.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 1029_BICJ-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 1029_BICJ-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% @chr1:189000001, elapsed 3.8s, est remaining 71.8s, peak mem 2275MB, user 66.7s, sys 1.5s, output queue size 42
progress 10% @chr2:94000001, elapsed 8.7s, est remaining 78.2s, peak mem 4199MB, user 221.9s, sys 4.5s, output queue size 172
progress 15% @chr2:172000001, elapsed 11.8s, est remaining 66.7s, peak mem 4584MB, user 332.9s, sys 6.3s, output queue size 328
progress 20% @chr3:149000001, elapsed 14.4s, est remaining 57.7s, peak mem 4688MB, user 412.8s, sys 7.0s, output queue size 489
progress 25% @chr4:124000001, elapsed 16.6s, est remaining 49.9s, peak mem 4764MB, user 474.5s, sys 7.5s, output queue size 650
progress 30% @chr5:38000001, elapsed 18.2s, est remaining 42.5s, peak mem 4764MB, user 537.9s, sys 8.2s, output queue size 464
progress 35% @chr6:27000001, elapsed 21.8s, est remaining 40.4s, peak mem 5043MB, user 624.2s, sys 8.8s, output queue size 625
progress 40% @chr6:163000001, elapsed 25.0s, est remaining 37.4s, peak mem 5408MB, user 726.4s, sys 9.4s, output queue size 197
progress 45% @chr8:70000001, elapsed 28.5s, est remaining 34.9s, peak mem 5672MB, user 827.1s, sys 10.2s, output queue size 357
progress 50% @chr9:91000001, elapsed 32.0s, est remaining 32.0s, peak mem 6041MB, user 952.4s, sys 11.2s, output queue size 187
progress 55% @chr10:68000001, elapsed 36.3s, est remaining 29.7s, peak mem 6496MB, user 1067.6s, sys 11.9s, output queue size 236
progress 60% @chr11:124000001, elapsed 39.3s, est remaining 26.2s, peak mem 6575MB, user 1164.9s, sys 12.5s, output queue size 312
progress 65% @chr11:77000001, elapsed 42.9s, est remaining 23.1s, peak mem 6680MB, user 1279.7s, sys 13.2s, output queue size 474
progress 70% @chr14:76000001, elapsed 45.6s, est remaining 19.6s, peak mem 6680MB, user 1349.7s, sys 13.8s, output queue size 635
progress 75% @chr16:42000001, elapsed 49.2s, est remaining 16.4s, peak mem 6680MB, user 1478.8s, sys 14.4s, output queue size 121
progress 80% @chr17:68000001, elapsed 54.4s, est remaining 13.6s, peak mem 6740MB, user 1624.2s, sys 15.3s, output queue size 189
progress 85% @chr19:47000001, elapsed 59.7s, est remaining 10.5s, peak mem 6861MB, user 1788.9s, sys 16.2s, output queue size 351
progress 90% @chr21:44000001, elapsed 63.0s, est remaining 7.0s, peak mem 6890MB, user 1913.0s, sys 16.9s, output queue size 78
progress 95% @chrY:52000001, elapsed 65.4s, est remaining 3.4s, peak mem 6890MB, user 1981.3s, sys 17.3s, output queue size 240
progress 100% @chr22:23000001, elapsed 70.9s, est remaining 0.0s, peak mem 7053MB, user 2040.7s, sys 17.8s, 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 806.340 user 14.577 sys 821.492 real
done: 1 calls 0.286 user 0.008 sys 0.303 real
exec_no_coor: 1 calls 0.005 user 0.011 sys 0.025 real
execute: 1 calls 0.006 user 0.003 sys 70.898 real
idle: 215 calls 0.141 user 0.001 sys 177.792 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 7396159488 mem 2042.759 user 18.188 sys 72.826 real