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/ff/cf8f9b380f888e2b3fb81c67bddd3f/.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/01/500ff411ac93a70f78f4f5a487b4e0/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/cf8f9b380f888e2b3fb81c67bddd3f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/500ff411ac93a70f78f4f5a487b4e0/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% @chr1:163000001, elapsed 0.0s, est remaining 0.5s, peak mem 114MB, user 0.1s, sys 0.4s, output queue size 34
progress 10% @chr2:75000001, elapsed 0.0s, est remaining 0.4s, peak mem 114MB, user 0.2s, sys 0.9s, output queue size 44
progress 15% @chr2:232000001, elapsed 0.1s, est remaining 0.4s, peak mem 114MB, user 0.2s, sys 1.5s, output queue size 3
progress 20% @chr3:148000001, elapsed 0.1s, est remaining 0.4s, peak mem 114MB, user 0.3s, sys 2.0s, output queue size 5
progress 25% @chr4:116000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.3s, sys 2.7s, output queue size 7
progress 30% @chr5:87000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.5s, sys 3.2s, output queue size 20
progress 35% @chr6:68000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.6s, sys 3.8s, output queue size 6
progress 40% @chr7:56000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.6s, sys 4.3s, output queue size 9
progress 45% @chr8:58000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.7s, sys 4.9s, output queue size 17
progress 50% @chr9:68000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.8s, sys 5.5s, output queue size 28
progress 55% @chr10:95000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.9s, sys 6.2s, output queue size 7
progress 60% @chr11:123000001, elapsed 0.3s, est remaining 0.2s, peak mem 114MB, user 1.0s, sys 6.7s, output queue size 14
progress 65% @chr13:16000001, elapsed 0.3s, est remaining 0.2s, peak mem 114MB, user 1.1s, sys 7.3s, output queue size 18
progress 70% @chr14:38000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 1.1s, sys 7.9s, output queue size 23
progress 75% @chr16:14000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 1.1s, sys 8.4s, output queue size 10
progress 80% @chr18:1, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 1.1s, sys 9.0s, output queue size 21
progress 85% @chr20:23000001, elapsed 0.4s, est remaining 0.1s, peak mem 114MB, user 1.2s, sys 9.7s, output queue size 13
progress 90% @chrX:39000001, elapsed 0.4s, est remaining 0.0s, peak mem 132MB, user 1.6s, sys 10.0s, output queue size 114
progress 95% @chrY:39000001, elapsed 0.4s, est remaining 0.0s, peak mem 147MB, user 1.9s, sys 10.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.0s, est remaining 0.0s, peak mem 165MB, user 3.6s, sys 11.0s, 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 384
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 51395347
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.216 user 5.650 sys 6.965 real
done: 1 calls 0.004 user 0.000 sys 0.008 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.001 user 0.000 sys 0.966 real
idle: 81 calls 0.013 user 0.031 sys 45.276 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 173170688 mem 4.087 user 11.858 sys 2.478 real