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/be/4c1ca1ec18c0ea4e6501925e2d7ca4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/7df0dd603900a4e96831ac49153a79/Sig_18_tissue.md.bam.bai
  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/be/4c1ca1ec18c0ea4e6501925e2d7ca4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/7df0dd603900a4e96831ac49153a79/Sig_18_tissue.md.bam
  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
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.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_tissue.md.bam --algo HsMetricAlgo --targets_list targets/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.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_tissue_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:156000001, elapsed 0.0s, est remaining 0.5s, peak mem 114MB, user 0.1s, sys 0.5s, output queue size 9
progress 10% @chr2:65000001, elapsed 0.1s, est remaining 0.5s, peak mem 114MB, user 0.2s, sys 1.2s, output queue size 11
progress 15% @chr2:229000001, elapsed 0.1s, est remaining 0.5s, peak mem 114MB, user 0.3s, sys 1.8s, output queue size 22
progress 20% @chr3:147000001, elapsed 0.1s, est remaining 0.4s, peak mem 114MB, user 0.4s, sys 2.5s, output queue size 7
progress 25% @chr4:104000001, elapsed 0.1s, est remaining 0.4s, peak mem 114MB, user 0.5s, sys 3.2s, output queue size 11
progress 30% @chr5:102000001, elapsed 0.2s, est remaining 0.4s, peak mem 114MB, user 0.5s, sys 3.9s, output queue size 8
progress 35% @chr6:56000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.6s, sys 4.6s, output queue size 31
progress 40% @chr7:50000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.7s, sys 5.2s, output queue size 14
progress 45% @chr8:47000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.8s, sys 6.0s, output queue size 10
progress 50% @chr9:92000001, elapsed 0.3s, est remaining 0.3s, peak mem 114MB, user 0.9s, sys 6.7s, output queue size 7
progress 55% @chr10:89000001, elapsed 0.3s, est remaining 0.2s, peak mem 114MB, user 0.9s, sys 7.4s, output queue size 29
progress 60% @chr11:115000001, elapsed 0.3s, est remaining 0.2s, peak mem 114MB, user 1.0s, sys 8.0s, output queue size 13
progress 65% @chr13:35000001, elapsed 0.3s, est remaining 0.2s, peak mem 114MB, user 1.1s, sys 8.8s, output queue size 7
progress 70% @chr14:81000001, elapsed 0.4s, est remaining 0.2s, peak mem 114MB, user 1.1s, sys 9.5s, output queue size 15
progress 75% @chr16:6000001, elapsed 0.4s, est remaining 0.1s, peak mem 114MB, user 1.2s, sys 10.2s, output queue size 7
progress 80% @chr17:80000001, elapsed 0.4s, est remaining 0.1s, peak mem 114MB, user 1.3s, sys 10.9s, output queue size 19
progress 85% @chr20:16000001, elapsed 0.4s, est remaining 0.1s, peak mem 114MB, user 1.4s, sys 11.6s, output queue size 8
progress 90% @chrX:41000001, elapsed 0.5s, est remaining 0.1s, peak mem 148MB, user 1.8s, sys 12.1s, output queue size 114
progress 95% @chrY:36000001, elapsed 0.5s, est remaining 0.0s, peak mem 168MB, user 2.4s, sys 12.5s, output queue size 271
progress 100% @chr21:41000001, elapsed 0.9s, est remaining 0.0s, peak mem 174MB, user 4.1s, sys 13.0s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50047062
reads: 1001838
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.382 user 6.511 sys 8.248 real
done: 1 calls 0.004 user 0.000 sys 0.009 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.001 sys 0.904 real
idle: 83 calls 0.009 user 0.015 sys 41.206 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 182734848 mem 4.620 user 13.631 sys 2.474 real