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/6e/031c787d8552986963520043944f7d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/a9e2ccd0c8e1b97d551b9ee4f0aee5/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/6e/031c787d8552986963520043944f7d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/a9e2ccd0c8e1b97d551b9ee4f0aee5/Sig_18_tissue.md.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_noncoding_postQC_hg38.bed
  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_tissue.md.bam --algo HsMetricAlgo --targets_list targets/altera_v3_targets_noncoding_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_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
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progress 5% @chr1:166000001, elapsed 1560.3s, est remaining 29645.3s, peak mem 102MB, user 0.1s, sys 1.2s, output queue size 21
progress 10% @chr2:76000001, elapsed 1560.3s, est remaining 14043.0s, peak mem 102MB, user 0.2s, sys 2.7s, output queue size 5
progress 15% @chr2:233000001, elapsed 1560.4s, est remaining 8842.1s, peak mem 102MB, user 0.3s, sys 4.1s, output queue size 2
progress 20% @chr3:160000001, elapsed 1560.4s, est remaining 6241.7s, peak mem 102MB, user 0.4s, sys 5.4s, output queue size 13
progress 25% @chr4:115000001, elapsed 1560.5s, est remaining 4681.4s, peak mem 102MB, user 0.5s, sys 6.9s, output queue size 14
progress 30% @chr5:71000001, elapsed 1560.5s, est remaining 3641.2s, peak mem 102MB, user 0.5s, sys 8.3s, output queue size 15
progress 35% @chr6:64000001, elapsed 1560.6s, est remaining 2898.2s, peak mem 102MB, user 0.7s, sys 9.6s, output queue size 13
progress 40% @chr7:55000001, elapsed 1560.6s, est remaining 2340.9s, peak mem 102MB, user 0.7s, sys 11.0s, output queue size 12
progress 45% @chr8:59000001, elapsed 1560.7s, est remaining 1907.5s, peak mem 102MB, user 0.8s, sys 12.4s, output queue size 16
progress 50% @chr9:60000001, elapsed 1560.7s, est remaining 1560.7s, peak mem 102MB, user 1.0s, sys 13.7s, output queue size 13
progress 55% @chr10:94000001, elapsed 1560.8s, est remaining 1277.0s, peak mem 102MB, user 1.1s, sys 15.0s, output queue size 11
progress 60% @chr11:106000001, elapsed 1560.8s, est remaining 1040.5s, peak mem 102MB, user 1.1s, sys 16.5s, output queue size 20
progress 65% @chr13:15000001, elapsed 1560.8s, est remaining 840.5s, peak mem 102MB, user 1.2s, sys 17.8s, output queue size 15
progress 70% @chr14:64000001, elapsed 1560.9s, est remaining 669.0s, peak mem 102MB, user 1.3s, sys 19.0s, output queue size 11
progress 75% @chr16:13000001, elapsed 1560.9s, est remaining 520.3s, peak mem 102MB, user 1.5s, sys 20.4s, output queue size 3
progress 80% @chr18:1, elapsed 1561.0s, est remaining 390.3s, peak mem 102MB, user 1.5s, sys 22.1s, output queue size 5
progress 85% @chr20:22000001, elapsed 1561.1s, est remaining 275.5s, peak mem 102MB, user 1.6s, sys 23.8s, output queue size 14
progress 90% @chrX:32000001, elapsed 1561.1s, est remaining 173.5s, peak mem 133MB, user 2.4s, sys 25.0s, output queue size 114
progress 95% @chrY:36000001, elapsed 1561.2s, est remaining 82.2s, peak mem 145MB, user 2.9s, sys 26.3s, output queue size 271
progress 100% @chr21:41000001, elapsed 1561.8s, est remaining 0.0s, peak mem 157MB, user 4.1s, sys 28.2s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 50047064
reads: 1001838
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.566 user 13.992 sys 16.637 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.001 sys 1561.790 real
idle: 61 calls 0.005 user 0.013 sys 46.072 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 165167104 mem 4.326 user 28.983 sys 1562.938 real