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/44/1e3b342b72b57fc2d40617ff75fd3e/.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/44/1e3b342b72b57fc2d40617ff75fd3e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/6deb667df284430001177d0a9637ad/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/6deb667df284430001177d0a9637ad/HCC1395_tumor.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_tumor.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_tumor_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 0.5s, peak mem 117MB, user 0.1s, sys 0.2s, output queue size 30
progress 10% @chr2:71000001, elapsed 0.0s, est remaining 0.4s, peak mem 117MB, user 0.3s, sys 0.8s, output queue size 19
progress 15% @chr2:239000001, elapsed 0.1s, est remaining 0.4s, peak mem 117MB, user 0.3s, sys 1.3s, output queue size 12
progress 20% @chr3:155000001, elapsed 0.1s, est remaining 0.3s, peak mem 117MB, user 0.4s, sys 2.0s, output queue size 17
progress 25% @chr4:91000001, elapsed 0.1s, est remaining 0.3s, peak mem 117MB, user 0.5s, sys 2.5s, output queue size 24
progress 30% @chr5:90000001, elapsed 0.1s, est remaining 0.3s, peak mem 117MB, user 0.6s, sys 3.0s, output queue size 20
progress 35% @chr6:67000001, elapsed 0.1s, est remaining 0.3s, peak mem 117MB, user 0.6s, sys 3.6s, output queue size 16
progress 40% @chr7:56000001, elapsed 0.2s, est remaining 0.3s, peak mem 117MB, user 0.7s, sys 4.2s, output queue size 15
progress 45% @chr8:60000001, elapsed 0.2s, est remaining 0.2s, peak mem 117MB, user 0.8s, sys 4.7s, output queue size 18
progress 50% @chr9:76000001, elapsed 0.2s, est remaining 0.2s, peak mem 117MB, user 0.8s, sys 5.2s, output queue size 26
progress 55% @chr10:66000001, elapsed 0.2s, est remaining 0.2s, peak mem 117MB, user 0.9s, sys 5.8s, output queue size 29
progress 60% @chr11:123000001, elapsed 0.3s, est remaining 0.2s, peak mem 117MB, user 0.9s, sys 6.3s, output queue size 18
progress 65% @chr13:15000001, elapsed 0.3s, est remaining 0.1s, peak mem 117MB, user 1.0s, sys 6.9s, output queue size 11
progress 70% @chr14:60000001, elapsed 0.3s, est remaining 0.1s, peak mem 117MB, user 1.1s, sys 7.6s, output queue size 16
progress 75% @chr16:15000001, elapsed 0.3s, est remaining 0.1s, peak mem 117MB, user 1.2s, sys 8.2s, output queue size 22
progress 80% @chr17:82000001, elapsed 0.3s, est remaining 0.1s, peak mem 117MB, user 1.2s, sys 8.7s, output queue size 10
progress 85% @chr20:22000001, elapsed 0.4s, est remaining 0.1s, peak mem 117MB, user 1.3s, sys 9.3s, output queue size 9
progress 90% @chrX:36000001, elapsed 0.4s, est remaining 0.0s, peak mem 135MB, user 1.6s, sys 9.6s, output queue size 114
progress 95% @chrY:40000001, elapsed 0.4s, est remaining 0.0s, peak mem 147MB, user 2.0s, sys 10.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 0.9s, est remaining 0.0s, peak mem 168MB, user 3.6s, sys 10.9s, 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: 50813895
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.416 user 5.338 sys 6.889 real
done: 1 calls 0.000 user 0.000 sys 0.009 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.004 user 0.003 sys 0.934 real
idle: 72 calls 0.008 user 0.014 sys 44.481 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 176254976 mem 4.182 user 11.665 sys 2.574 real