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/e2/4bea5d99713331d5873abd3f491b4a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/1da352571a0470ddf30af8993404ce/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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_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/3f/1da352571a0470ddf30af8993404ce/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/4bea5d99713331d5873abd3f491b4a/.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 FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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 FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1_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% @chr1:173000001, elapsed 5.0s, est remaining 94.4s, peak mem 3818MB, user 111.3s, sys 3.4s, output queue size 146
progress 10% @chr2:84000001, elapsed 9.1s, est remaining 81.9s, peak mem 5508MB, user 239.2s, sys 5.4s, output queue size 166
progress 15% @chr3:17000001, elapsed 13.4s, est remaining 76.1s, peak mem 8291MB, user 356.0s, sys 7.4s, output queue size 220
progress 20% @chr3:178000001, elapsed 16.9s, est remaining 67.5s, peak mem 9718MB, user 471.5s, sys 9.1s, output queue size 364
progress 25% @chr4:133000001, elapsed 19.9s, est remaining 59.6s, peak mem 9838MB, user 573.0s, sys 12.3s, output queue size 302
progress 30% @chr5:83000001, elapsed 22.2s, est remaining 51.7s, peak mem 9838MB, user 637.2s, sys 12.7s, output queue size 464
progress 35% @chr6:86000001, elapsed 25.9s, est remaining 48.1s, peak mem 9838MB, user 745.0s, sys 13.4s, output queue size 625
progress 40% @chr7:66000001, elapsed 30.3s, est remaining 45.4s, peak mem 10039MB, user 852.7s, sys 14.1s, output queue size 786
progress 45% @chr8:83000001, elapsed 35.5s, est remaining 43.3s, peak mem 10453MB, user 1020.0s, sys 15.1s, output queue size 204
progress 50% @chr9:21000001, elapsed 39.6s, est remaining 39.6s, peak mem 10506MB, user 1132.9s, sys 15.9s, output queue size 366
progress 55% @chr10:99000001, elapsed 44.4s, est remaining 36.3s, peak mem 10669MB, user 1287.5s, sys 16.9s, output queue size 348
progress 60% @chr11:130000001, elapsed 49.7s, est remaining 33.1s, peak mem 10690MB, user 1444.5s, sys 17.6s, output queue size 510
progress 65% @chr13:39000001, elapsed 54.3s, est remaining 29.3s, peak mem 10958MB, user 1585.3s, sys 18.5s, output queue size 672
progress 70% @chr14:85000001, elapsed 56.9s, est remaining 24.4s, peak mem 10989MB, user 1686.0s, sys 19.1s, output queue size 635
progress 75% @chr16:42000001, elapsed 62.2s, est remaining 20.7s, peak mem 11117MB, user 1843.7s, sys 19.8s, output queue size 461
progress 80% @chr18:28000001, elapsed 71.0s, est remaining 17.7s, peak mem 11291MB, user 2060.8s, sys 21.2s, output queue size 623
progress 85% @chr20:23000001, elapsed 79.1s, est remaining 14.0s, peak mem 11368MB, user 2328.4s, sys 22.5s, output queue size 785
progress 90% @chrX:34000001, elapsed 83.4s, est remaining 9.3s, peak mem 11408MB, user 2504.2s, sys 23.4s, output queue size 513
progress 95% @chrY:55000001, elapsed 86.1s, est remaining 4.5s, peak mem 11408MB, user 2574.6s, sys 23.9s, output queue size 675
progress 100% @chr22:23000001, elapsed 95.4s, est remaining 0.0s, peak mem 11408MB, user 2702.3s, sys 24.6s, output queue size 3635
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 68397013038
reads: 1261745363
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1074.658 user 21.911 sys 1098.039 real
done: 1 calls 0.397 user 0.020 sys 0.423 real
exec_no_coor: 1 calls 0.009 user 0.000 sys 0.018 real
execute: 1 calls 0.001 user 0.001 sys 95.422 real
idle: 296 calls 0.143 user 0.001 sys 261.387 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 11962937344 mem 2704.637 user 25.287 sys 97.298 real