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/a5/81b467e47a2f70b26b2d790344109d/.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/e5/5e14d3c54516fce231a15f3d7307d2/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/81b467e47a2f70b26b2d790344109d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/5e14d3c54516fce231a15f3d7307d2/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% @chr1:162000001, elapsed 0.0s, est remaining 0.4s, peak mem 120MB, user 0.1s, sys 0.3s, output queue size 17
progress 10% @chr2:56000001, elapsed 0.0s, est remaining 0.4s, peak mem 120MB, user 0.2s, sys 0.8s, output queue size 17
progress 15% @chr2:235000001, elapsed 0.1s, est remaining 0.4s, peak mem 120MB, user 0.2s, sys 1.3s, output queue size 17
progress 20% @chr3:158000001, elapsed 0.1s, est remaining 0.3s, peak mem 121MB, user 0.3s, sys 1.8s, output queue size 6
progress 25% @chr4:97000001, elapsed 0.1s, est remaining 0.3s, peak mem 121MB, user 0.4s, sys 2.4s, output queue size 19
progress 30% @chr5:89000001, elapsed 0.1s, est remaining 0.3s, peak mem 121MB, user 0.4s, sys 2.9s, output queue size 16
progress 35% @chr6:67000001, elapsed 0.1s, est remaining 0.3s, peak mem 121MB, user 0.5s, sys 3.4s, output queue size 7
progress 40% @chr7:41000001, elapsed 0.2s, est remaining 0.2s, peak mem 121MB, user 0.6s, sys 4.0s, output queue size 15
progress 45% @chr8:59000001, elapsed 0.2s, est remaining 0.2s, peak mem 121MB, user 0.7s, sys 4.5s, output queue size 17
progress 50% @chr9:75000001, elapsed 0.2s, est remaining 0.2s, peak mem 121MB, user 0.8s, sys 5.0s, output queue size 13
progress 55% @chr10:100000001, elapsed 0.2s, est remaining 0.2s, peak mem 121MB, user 0.9s, sys 5.5s, output queue size 18
progress 60% @chr11:123000001, elapsed 0.2s, est remaining 0.2s, peak mem 121MB, user 0.9s, sys 6.1s, output queue size 22
progress 65% @chr13:20000001, elapsed 0.3s, est remaining 0.1s, peak mem 121MB, user 1.0s, sys 6.6s, output queue size 5
progress 70% @chr14:65000001, elapsed 0.3s, est remaining 0.1s, peak mem 121MB, user 1.1s, sys 7.1s, output queue size 12
progress 75% @chr16:14000001, elapsed 0.3s, est remaining 0.1s, peak mem 121MB, user 1.2s, sys 7.6s, output queue size 14
progress 80% @chr18:2000001, elapsed 0.3s, est remaining 0.1s, peak mem 121MB, user 1.3s, sys 8.1s, output queue size 14
progress 85% @chr20:4000001, elapsed 0.3s, est remaining 0.1s, peak mem 121MB, user 1.4s, sys 8.7s, output queue size 18
progress 90% @chrX:41000001, elapsed 0.4s, est remaining 0.0s, peak mem 162MB, user 1.7s, sys 9.0s, output queue size 114
progress 95% @chrY:39000001, elapsed 0.4s, est remaining 0.0s, peak mem 181MB, user 2.1s, sys 9.3s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.0s, est remaining 0.0s, peak mem 206MB, user 4.5s, sys 9.7s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 64
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 51395354
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.690 user 5.010 sys 6.760 real
done: 1 calls 0.011 user 0.000 sys 0.011 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.004 user 0.002 sys 0.994 real
idle: 72 calls 0.024 user 0.022 sys 46.631 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 217731072 mem 5.072 user 10.433 sys 2.587 real