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/b1/b829a9f97554fca465e69890c5cf6e/.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/b1/b829a9f97554fca465e69890c5cf6e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/1522110040efeb211ec882b01ba433/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/1522110040efeb211ec882b01ba433/Sig_18_Blood.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 Sig_18_Blood.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 Sig_18_Blood_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% @chr1:143000001, elapsed 0.1s, est remaining 1.3s, peak mem 114MB, user 0.1s, sys 1.5s, output queue size 36
progress 10% @chr2:54000001, elapsed 0.1s, est remaining 1.2s, peak mem 114MB, user 0.2s, sys 3.2s, output queue size 33
progress 15% @chr3:14000001, elapsed 0.2s, est remaining 1.1s, peak mem 114MB, user 0.3s, sys 5.2s, output queue size 17
progress 20% @chr3:181000001, elapsed 0.3s, est remaining 1.0s, peak mem 114MB, user 0.3s, sys 6.9s, output queue size 18
progress 25% @chr4:138000001, elapsed 0.3s, est remaining 0.9s, peak mem 114MB, user 0.5s, sys 8.6s, output queue size 37
progress 30% @chr5:70000001, elapsed 0.4s, est remaining 0.9s, peak mem 114MB, user 0.6s, sys 10.4s, output queue size 27
progress 35% @chr6:53000001, elapsed 0.4s, est remaining 0.8s, peak mem 114MB, user 0.7s, sys 12.2s, output queue size 36
progress 40% @chr7:80000001, elapsed 0.5s, est remaining 0.7s, peak mem 114MB, user 0.9s, sys 13.8s, output queue size 37
progress 45% @chr8:78000001, elapsed 0.6s, est remaining 0.7s, peak mem 114MB, user 1.2s, sys 15.5s, output queue size 45
progress 50% @chr9:92000001, elapsed 0.6s, est remaining 0.6s, peak mem 114MB, user 1.3s, sys 17.2s, output queue size 51
progress 55% @chr10:44000001, elapsed 0.7s, est remaining 0.6s, peak mem 114MB, user 1.3s, sys 19.0s, output queue size 51
progress 60% @chr11:103000001, elapsed 0.7s, est remaining 0.5s, peak mem 114MB, user 1.4s, sys 20.7s, output queue size 20
progress 65% @chr13:36000001, elapsed 0.8s, est remaining 0.4s, peak mem 114MB, user 1.5s, sys 22.3s, output queue size 15
progress 70% @chr14:50000001, elapsed 0.8s, est remaining 0.4s, peak mem 114MB, user 1.7s, sys 24.0s, output queue size 17
progress 75% @chr15:98000001, elapsed 0.9s, est remaining 0.3s, peak mem 114MB, user 1.7s, sys 25.6s, output queue size 17
progress 80% @chr17:69000001, elapsed 1.0s, est remaining 0.2s, peak mem 114MB, user 1.9s, sys 27.2s, output queue size 21
progress 85% @chr20:3000001, elapsed 1.0s, est remaining 0.2s, peak mem 114MB, user 2.0s, sys 28.8s, output queue size 20
progress 90% @chrX:29000001, elapsed 1.1s, est remaining 0.1s, peak mem 129MB, user 2.6s, sys 29.9s, output queue size 114
progress 95% @chrY:45000001, elapsed 1.2s, est remaining 0.1s, peak mem 138MB, user 3.0s, sys 31.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.8s, est remaining 0.0s, peak mem 162MB, user 4.4s, sys 34.3s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 52290599
reads: 1001133
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.111 user 18.410 sys 18.713 real
done: 1 calls 0.002 user 0.000 sys 0.010 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.003 sys 1.780 real
idle: 77 calls 0.004 user 0.025 sys 45.782 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 169959424 mem 4.830 user 35.090 sys 3.272 real