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/8a/cfd7777c714bd5cb6a9e5cb7fdfafa/.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/8a/cfd7777c714bd5cb6a9e5cb7fdfafa/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/f84457a21aa906d2a86c8a3c95aa99/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/f84457a21aa906d2a86c8a3c95aa99/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% @chr1:157000001, elapsed 0.0s, est remaining 0.4s, peak mem 115MB, user 0.0s, sys 0.3s, output queue size 4
progress 10% @chr2:71000001, elapsed 0.0s, est remaining 0.4s, peak mem 115MB, user 0.1s, sys 0.9s, output queue size 23
progress 15% @chr3:11000001, elapsed 0.1s, est remaining 0.4s, peak mem 115MB, user 0.2s, sys 1.3s, output queue size 4
progress 20% @chr3:172000001, elapsed 0.1s, est remaining 0.3s, peak mem 115MB, user 0.3s, sys 1.8s, output queue size 23
progress 25% @chr4:110000001, elapsed 0.1s, est remaining 0.3s, peak mem 115MB, user 0.4s, sys 2.4s, output queue size 5
progress 30% @chr5:83000001, elapsed 0.1s, est remaining 0.3s, peak mem 115MB, user 0.5s, sys 2.9s, output queue size 7
progress 35% @chr6:63000001, elapsed 0.1s, est remaining 0.3s, peak mem 115MB, user 0.6s, sys 3.4s, output queue size 33
progress 40% @chr7:50000001, elapsed 0.2s, est remaining 0.3s, peak mem 115MB, user 0.6s, sys 4.0s, output queue size 5
progress 45% @chr8:54000001, elapsed 0.2s, est remaining 0.2s, peak mem 115MB, user 0.7s, sys 4.6s, output queue size 19
progress 50% @chr9:69000001, elapsed 0.2s, est remaining 0.2s, peak mem 115MB, user 0.7s, sys 5.1s, output queue size 4
progress 55% @chr10:90000001, elapsed 0.2s, est remaining 0.2s, peak mem 115MB, user 0.8s, sys 5.6s, output queue size 21
progress 60% @chr12:1000001, elapsed 0.2s, est remaining 0.2s, peak mem 115MB, user 0.8s, sys 6.1s, output queue size 5
progress 65% @chr13:33000001, elapsed 0.3s, est remaining 0.1s, peak mem 115MB, user 0.9s, sys 6.7s, output queue size 15
progress 70% @chr14:57000001, elapsed 0.3s, est remaining 0.1s, peak mem 115MB, user 1.0s, sys 7.2s, output queue size 9
progress 75% @chr16:13000001, elapsed 0.3s, est remaining 0.1s, peak mem 115MB, user 1.0s, sys 7.8s, output queue size 11
progress 80% @chr17:77000001, elapsed 0.3s, est remaining 0.1s, peak mem 115MB, user 1.1s, sys 8.3s, output queue size 7
progress 85% @chr20:21000001, elapsed 0.4s, est remaining 0.1s, peak mem 115MB, user 1.2s, sys 8.8s, output queue size 6
progress 90% @chrX:42000001, elapsed 0.4s, est remaining 0.0s, peak mem 137MB, user 1.5s, sys 9.2s, output queue size 114
progress 95% @chrY:39000001, elapsed 0.4s, est remaining 0.0s, peak mem 158MB, user 2.0s, sys 9.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.0s, est remaining 0.0s, peak mem 176MB, user 3.7s, sys 10.2s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 52290600
reads: 1001133
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.113 user 5.023 sys 6.766 real
done: 1 calls 0.005 user 0.000 sys 0.010 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.001 user 0.000 sys 0.974 real
idle: 76 calls 0.015 user 0.027 sys 46.046 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 186793984 mem 4.311 user 10.847 sys 2.492 real