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/77/33f80dd6cf6fc6721b53fb738ed210/.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/74/ea7a515a2f70db517a2c1354a35f6b/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/33f80dd6cf6fc6721b53fb738ed210/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/ea7a515a2f70db517a2c1354a35f6b/HCC1395_BL.md.bam.bai
  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 HCC1395_BL.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 HCC1395_BL_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% @chr1:163000001, elapsed 0.0s, est remaining 0.4s, peak mem 114MB, user 0.1s, sys 0.4s, output queue size 16
progress 10% @chr2:71000001, elapsed 0.0s, est remaining 0.4s, peak mem 114MB, user 0.2s, sys 0.8s, output queue size 2
progress 15% @chr2:238000001, elapsed 0.1s, est remaining 0.4s, peak mem 114MB, user 0.4s, sys 1.3s, output queue size 10
progress 20% @chr3:156000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.4s, sys 1.8s, output queue size 18
progress 25% @chr4:103000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.4s, sys 2.5s, output queue size 16
progress 30% @chr5:86000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.5s, sys 3.0s, output queue size 22
progress 35% @chr6:65000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.6s, sys 3.6s, output queue size 14
progress 40% @chr7:58000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.7s, sys 4.0s, output queue size 10
progress 45% @chr8:59000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.8s, sys 4.5s, output queue size 8
progress 50% @chr9:77000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.8s, sys 5.1s, output queue size 20
progress 55% @chr10:96000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.9s, sys 5.6s, output queue size 16
progress 60% @chr11:123000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.9s, sys 6.2s, output queue size 23
progress 65% @chr13:13000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 1.0s, sys 6.7s, output queue size 7
progress 70% @chr14:65000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 1.1s, sys 7.2s, output queue size 21
progress 75% @chr16:14000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 1.2s, sys 7.7s, output queue size 10
progress 80% @chr18:2000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 1.2s, sys 8.3s, output queue size 17
progress 85% @chr20:25000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 1.4s, sys 8.8s, output queue size 22
progress 90% @chrX:39000001, elapsed 0.4s, est remaining 0.0s, peak mem 132MB, user 1.7s, sys 9.1s, output queue size 114
progress 95% @chrY:38000001, elapsed 0.4s, est remaining 0.0s, peak mem 150MB, user 2.0s, sys 9.5s, output queue size 276
progress 100% @chr21:41000001, elapsed 0.9s, est remaining 0.0s, peak mem 168MB, user 3.7s, sys 10.3s, output queue size 3664
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 384
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 51395364
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.205 user 5.158 sys 6.703 real
done: 1 calls 0.001 user 0.000 sys 0.007 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.004 sys 0.941 real
idle: 79 calls 0.015 user 0.023 sys 45.279 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 176308224 mem 4.185 user 11.067 sys 2.451 real