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/d2/179a8b629b6eaecea05c9bc2f185c7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.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/47/4bec5ec8a6cdcb74a1f00581238e86/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/179a8b629b6eaecea05c9bc2f185c7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/4bec5ec8a6cdcb74a1f00581238e86/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-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.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-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 0.0s, est remaining 0.4s, peak mem 113MB, user 0.1s, sys 0.2s, output queue size 3
progress 10% @chr2:72000001, elapsed 0.0s, est remaining 0.4s, peak mem 113MB, user 0.2s, sys 0.7s, output queue size 1
progress 15% @chr2:233000001, elapsed 0.1s, est remaining 0.4s, peak mem 113MB, user 0.3s, sys 1.2s, output queue size 2
progress 20% @chr3:152000001, elapsed 0.1s, est remaining 0.3s, peak mem 113MB, user 0.4s, sys 1.7s, output queue size 1
progress 25% @chr4:115000001, elapsed 0.1s, est remaining 0.3s, peak mem 113MB, user 0.5s, sys 2.2s, output queue size 19
progress 30% @chr5:86000001, elapsed 0.1s, est remaining 0.3s, peak mem 113MB, user 0.5s, sys 2.7s, output queue size 15
progress 35% @chr6:67000001, elapsed 0.1s, est remaining 0.3s, peak mem 113MB, user 0.6s, sys 3.3s, output queue size 12
progress 40% @chr7:57000001, elapsed 0.2s, est remaining 0.2s, peak mem 113MB, user 0.7s, sys 3.8s, output queue size 8
progress 45% @chr8:59000001, elapsed 0.2s, est remaining 0.2s, peak mem 113MB, user 0.7s, sys 4.3s, output queue size 8
progress 50% @chr9:74000001, elapsed 0.2s, est remaining 0.2s, peak mem 113MB, user 0.8s, sys 4.9s, output queue size 8
progress 55% @chr10:97000001, elapsed 0.2s, est remaining 0.2s, peak mem 113MB, user 0.8s, sys 5.4s, output queue size 5
progress 60% @chr11:123000001, elapsed 0.2s, est remaining 0.2s, peak mem 113MB, user 0.9s, sys 6.0s, output queue size 9
progress 65% @chr13:16000001, elapsed 0.3s, est remaining 0.1s, peak mem 113MB, user 1.0s, sys 6.5s, output queue size 7
progress 70% @chr14:62000001, elapsed 0.3s, est remaining 0.1s, peak mem 113MB, user 1.0s, sys 7.1s, output queue size 14
progress 75% @chr16:14000001, elapsed 0.3s, est remaining 0.1s, peak mem 113MB, user 1.0s, sys 7.6s, output queue size 14
progress 80% @chr17:78000001, elapsed 0.3s, est remaining 0.1s, peak mem 113MB, user 1.2s, sys 8.1s, output queue size 24
progress 85% @chr20:23000001, elapsed 0.3s, est remaining 0.1s, peak mem 113MB, user 1.2s, sys 8.7s, output queue size 22
progress 90% @chr21:13000001, elapsed 0.4s, est remaining 0.0s, peak mem 140MB, user 1.6s, sys 8.9s, output queue size 114
progress 95% @chrY:38000001, elapsed 0.4s, est remaining 0.0s, peak mem 157MB, user 1.8s, sys 9.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 0.9s, est remaining 0.0s, peak mem 178MB, user 3.6s, sys 9.9s, 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: 51395954
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.271 user 4.835 sys 6.423 real
done: 1 calls 0.000 user 0.006 sys 0.007 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.003 sys 0.915 real
idle: 76 calls 0.012 user 0.026 sys 45.027 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 188641280 mem 3.975 user 10.574 sys 2.398 real