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/7d/3b0490f8c3ba14a96d04d3c6c998df/.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/59/bc5e7b7f2c48b2e51fd97162601462/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/3b0490f8c3ba14a96d04d3c6c998df/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/bc5e7b7f2c48b2e51fd97162601462/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% @chr1:156000001, elapsed 0.1s, est remaining 1.2s, peak mem 117MB, user 0.2s, sys 1.3s, output queue size 5
progress 10% @chr2:56000001, elapsed 0.1s, est remaining 1.1s, peak mem 117MB, user 0.4s, sys 3.0s, output queue size 17
progress 15% @chr2:227000001, elapsed 0.2s, est remaining 1.0s, peak mem 117MB, user 0.5s, sys 4.6s, output queue size 8
progress 20% @chr3:152000001, elapsed 0.2s, est remaining 0.9s, peak mem 117MB, user 0.7s, sys 6.2s, output queue size 8
progress 25% @chr4:115000001, elapsed 0.3s, est remaining 0.9s, peak mem 117MB, user 0.9s, sys 7.7s, output queue size 5
progress 30% @chr5:88000001, elapsed 0.4s, est remaining 0.8s, peak mem 117MB, user 1.0s, sys 9.3s, output queue size 10
progress 35% @chr6:62000001, elapsed 0.4s, est remaining 0.8s, peak mem 117MB, user 1.1s, sys 11.1s, output queue size 11
progress 40% @chr7:51000001, elapsed 0.5s, est remaining 0.7s, peak mem 117MB, user 1.1s, sys 12.8s, output queue size 13
progress 45% @chr8:43000001, elapsed 0.5s, est remaining 0.6s, peak mem 117MB, user 1.3s, sys 14.5s, output queue size 14
progress 50% @chr9:71000001, elapsed 0.6s, est remaining 0.6s, peak mem 117MB, user 1.3s, sys 16.2s, output queue size 8
progress 55% @chr10:89000001, elapsed 0.6s, est remaining 0.5s, peak mem 117MB, user 1.5s, sys 17.8s, output queue size 7
progress 60% @chr11:125000001, elapsed 0.7s, est remaining 0.5s, peak mem 117MB, user 1.7s, sys 19.4s, output queue size 5
progress 65% @chr13:15000001, elapsed 0.8s, est remaining 0.4s, peak mem 117MB, user 2.0s, sys 20.9s, output queue size 4
progress 70% @chr14:60000001, elapsed 0.8s, est remaining 0.3s, peak mem 117MB, user 2.4s, sys 22.2s, output queue size 14
progress 75% @chr16:17000001, elapsed 0.9s, est remaining 0.3s, peak mem 117MB, user 2.5s, sys 23.8s, output queue size 4
progress 80% @chr17:77000001, elapsed 0.9s, est remaining 0.2s, peak mem 117MB, user 2.8s, sys 25.3s, output queue size 7
progress 85% @chr20:13000001, elapsed 1.0s, est remaining 0.2s, peak mem 117MB, user 3.0s, sys 27.0s, output queue size 11
progress 90% @chrX:35000001, elapsed 1.1s, est remaining 0.1s, peak mem 120MB, user 3.5s, sys 28.3s, output queue size 114
progress 95% @chrY:26000001, elapsed 1.2s, est remaining 0.1s, peak mem 138MB, user 4.1s, sys 30.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.8s, est remaining 0.0s, peak mem 165MB, user 5.8s, sys 33.0s, 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: 51395360
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.322 user 18.030 sys 18.404 real
done: 1 calls 0.010 user 0.000 sys 0.013 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.001 sys 1.782 real
idle: 76 calls 0.006 user 0.022 sys 46.023 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 173105152 mem 6.334 user 33.832 sys 3.329 real