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/2c/a7a32d12b22079ed79df9bce6e34e3/.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/4b/77f7ae6d2659ec7c056abb9c1117b6/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/a7a32d12b22079ed79df9bce6e34e3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/77f7ae6d2659ec7c056abb9c1117b6/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% @chr1:162000001, elapsed 0.0s, est remaining 0.7s, peak mem 108MB, user 0.6s, sys 0.1s, output queue size 21
progress 10% @chr2:76000001, elapsed 0.1s, est remaining 0.6s, peak mem 108MB, user 1.0s, sys 0.8s, output queue size 17
progress 15% @chr2:231000001, elapsed 0.1s, est remaining 0.6s, peak mem 108MB, user 1.5s, sys 1.4s, output queue size 5
progress 20% @chr3:153000001, elapsed 0.1s, est remaining 0.6s, peak mem 108MB, user 1.8s, sys 2.1s, output queue size 3
progress 25% @chr4:117000001, elapsed 0.2s, est remaining 0.5s, peak mem 108MB, user 2.2s, sys 2.8s, output queue size 1
progress 30% @chr5:84000001, elapsed 0.2s, est remaining 0.5s, peak mem 108MB, user 2.4s, sys 3.5s, output queue size 9
progress 35% @chr6:63000001, elapsed 0.2s, est remaining 0.4s, peak mem 108MB, user 3.0s, sys 3.9s, output queue size 2
progress 40% @chr7:60000001, elapsed 0.3s, est remaining 0.4s, peak mem 108MB, user 3.5s, sys 4.5s, output queue size 5
progress 45% @chr8:51000001, elapsed 0.3s, est remaining 0.4s, peak mem 108MB, user 3.8s, sys 5.3s, output queue size 8
progress 50% @chr9:70000001, elapsed 0.3s, est remaining 0.3s, peak mem 108MB, user 4.2s, sys 6.0s, output queue size 5
progress 55% @chr10:89000001, elapsed 0.4s, est remaining 0.3s, peak mem 108MB, user 4.5s, sys 7.1s, output queue size 6
progress 60% @chr11:118000001, elapsed 0.4s, est remaining 0.3s, peak mem 108MB, user 4.8s, sys 8.2s, output queue size 13
progress 65% @chr13:2000001, elapsed 0.5s, est remaining 0.3s, peak mem 111MB, user 5.0s, sys 9.6s, output queue size 13
progress 70% @chr14:55000001, elapsed 0.5s, est remaining 0.2s, peak mem 111MB, user 5.2s, sys 10.9s, output queue size 6
progress 75% @chr16:8000001, elapsed 0.6s, est remaining 0.2s, peak mem 111MB, user 5.5s, sys 12.2s, output queue size 8
progress 80% @chr17:81000001, elapsed 0.6s, est remaining 0.2s, peak mem 111MB, user 5.7s, sys 13.4s, output queue size 8
progress 85% @chr20:17000001, elapsed 0.7s, est remaining 0.1s, peak mem 111MB, user 5.9s, sys 14.9s, output queue size 7
progress 90% @chrX:36000001, elapsed 0.8s, est remaining 0.1s, peak mem 126MB, user 6.2s, sys 15.8s, output queue size 114
progress 95% @chr21:36000001, elapsed 0.8s, est remaining 0.0s, peak mem 144MB, user 6.7s, sys 16.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.3s, est remaining 0.0s, peak mem 162MB, user 8.2s, sys 17.8s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 51395357
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.362 user 8.831 sys 10.675 real
done: 1 calls 0.014 user 0.000 sys 0.015 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.001 sys 1.343 real
idle: 73 calls 0.015 user 0.016 sys 45.295 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 169967616 mem 8.804 user 18.472 sys 2.874 real