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/4e/838622b85ffb04ff3ee78fcd0d3b3f/.command.sh
  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_footprint.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/4e/838622b85ffb04ff3ee78fcd0d3b3f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/57a16f0cfbc17f3f3dcbee22c14121/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/57a16f0cfbc17f3f3dcbee22c14121/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_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.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_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:167000001, elapsed 0.0s, est remaining 0.6s, peak mem 118MB, user 0.1s, sys 0.4s, output queue size 12
progress 10% @chr2:77000001, elapsed 0.1s, est remaining 0.5s, peak mem 118MB, user 0.2s, sys 1.2s, output queue size 31
progress 15% @chr2:236000001, elapsed 0.1s, est remaining 0.5s, peak mem 118MB, user 0.3s, sys 1.9s, output queue size 18
progress 20% @chr3:156000001, elapsed 0.1s, est remaining 0.4s, peak mem 118MB, user 0.4s, sys 2.6s, output queue size 19
progress 25% @chr4:115000001, elapsed 0.1s, est remaining 0.4s, peak mem 118MB, user 0.4s, sys 3.4s, output queue size 17
progress 30% @chr5:86000001, elapsed 0.2s, est remaining 0.4s, peak mem 118MB, user 0.6s, sys 4.1s, output queue size 24
progress 35% @chr6:69000001, elapsed 0.2s, est remaining 0.4s, peak mem 118MB, user 0.7s, sys 4.6s, output queue size 5
progress 40% @chr7:59000001, elapsed 0.2s, est remaining 0.3s, peak mem 118MB, user 0.8s, sys 5.4s, output queue size 13
progress 45% @chr8:52000001, elapsed 0.2s, est remaining 0.3s, peak mem 118MB, user 0.8s, sys 6.2s, output queue size 17
progress 50% @chr9:76000001, elapsed 0.3s, est remaining 0.3s, peak mem 118MB, user 1.0s, sys 6.7s, output queue size 17
progress 55% @chr10:96000001, elapsed 0.3s, est remaining 0.2s, peak mem 118MB, user 1.2s, sys 7.5s, output queue size 13
progress 60% @chr11:117000001, elapsed 0.3s, est remaining 0.2s, peak mem 118MB, user 1.3s, sys 8.0s, output queue size 13
progress 65% @chr13:15000001, elapsed 0.3s, est remaining 0.2s, peak mem 118MB, user 1.4s, sys 8.8s, output queue size 13
progress 70% @chr14:63000001, elapsed 0.4s, est remaining 0.2s, peak mem 118MB, user 1.5s, sys 9.4s, output queue size 13
progress 75% @chr16:13000001, elapsed 0.4s, est remaining 0.1s, peak mem 118MB, user 1.5s, sys 10.2s, output queue size 2
progress 80% @chr18:4000001, elapsed 0.4s, est remaining 0.1s, peak mem 118MB, user 1.6s, sys 11.0s, output queue size 17
progress 85% @chr20:27000001, elapsed 0.5s, est remaining 0.1s, peak mem 118MB, user 1.6s, sys 11.6s, output queue size 12
progress 90% @chrX:40000001, elapsed 0.5s, est remaining 0.1s, peak mem 145MB, user 2.0s, sys 12.1s, output queue size 114
progress 95% @chrY:41000001, elapsed 0.5s, est remaining 0.0s, peak mem 160MB, user 2.2s, sys 12.5s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.1s, est remaining 0.0s, peak mem 183MB, user 4.3s, sys 13.2s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 51394915
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.164 user 6.404 sys 8.246 real
done: 1 calls 0.008 user 0.000 sys 0.014 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.007 user 0.002 sys 1.074 real
idle: 74 calls 0.012 user 0.020 sys 45.546 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 193748992 mem 4.873 user 13.932 sys 2.610 real