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/1d/95292a1c1dad82955aad0ab8ba0459/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/8467a0f89a3b28cafdce3f1ccefdce/Sig_18_tissue.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_footprint.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/1d/95292a1c1dad82955aad0ab8ba0459/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/8467a0f89a3b28cafdce3f1ccefdce/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
==> 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_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.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_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:146000001, elapsed 0.1s, est remaining 1.7s, peak mem 117MB, user 0.1s, sys 2.0s, output queue size 17
progress 10% @chr2:60000001, elapsed 0.2s, est remaining 1.4s, peak mem 117MB, user 0.3s, sys 4.1s, output queue size 17
progress 15% @chr2:218000001, elapsed 0.2s, est remaining 1.3s, peak mem 117MB, user 0.3s, sys 6.1s, output queue size 17
progress 20% @chr3:138000001, elapsed 0.3s, est remaining 1.2s, peak mem 117MB, user 0.4s, sys 8.2s, output queue size 19
progress 25% @chr4:134000001, elapsed 0.4s, est remaining 1.1s, peak mem 117MB, user 0.5s, sys 10.2s, output queue size 15
progress 30% @chr5:72000001, elapsed 0.4s, est remaining 1.0s, peak mem 117MB, user 0.5s, sys 12.2s, output queue size 14
progress 35% @chr6:58000001, elapsed 0.5s, est remaining 0.9s, peak mem 117MB, user 0.6s, sys 14.2s, output queue size 25
progress 40% @chr7:49000001, elapsed 0.6s, est remaining 0.8s, peak mem 117MB, user 0.7s, sys 16.2s, output queue size 33
progress 45% @chr8:48000001, elapsed 0.6s, est remaining 0.8s, peak mem 117MB, user 0.8s, sys 18.1s, output queue size 26
progress 50% @chr9:63000001, elapsed 0.7s, est remaining 0.7s, peak mem 117MB, user 0.9s, sys 20.2s, output queue size 19
progress 55% @chr10:119000001, elapsed 0.8s, est remaining 0.6s, peak mem 117MB, user 1.0s, sys 22.1s, output queue size 17
progress 60% @chr11:101000001, elapsed 0.8s, est remaining 0.6s, peak mem 117MB, user 1.1s, sys 24.1s, output queue size 22
progress 65% @chr13:4000001, elapsed 0.9s, est remaining 0.5s, peak mem 117MB, user 1.1s, sys 26.1s, output queue size 11
progress 70% @chr14:51000001, elapsed 1.0s, est remaining 0.4s, peak mem 117MB, user 1.1s, sys 28.1s, output queue size 15
progress 75% @chr15:100000001, elapsed 1.0s, est remaining 0.3s, peak mem 117MB, user 1.2s, sys 30.1s, output queue size 15
progress 80% @chr17:72000001, elapsed 1.1s, est remaining 0.3s, peak mem 117MB, user 1.3s, sys 32.0s, output queue size 14
progress 85% @chr20:9000001, elapsed 1.2s, est remaining 0.2s, peak mem 117MB, user 1.4s, sys 34.1s, output queue size 16
progress 90% @chrX:35000001, elapsed 1.3s, est remaining 0.1s, peak mem 132MB, user 1.9s, sys 35.2s, output queue size 114
progress 95% @chrY:52000001, elapsed 1.3s, est remaining 0.1s, peak mem 144MB, user 2.5s, sys 37.1s, output queue size 271
progress 100% @chr21:41000001, elapsed 2.0s, est remaining 0.0s, peak mem 159MB, user 4.1s, sys 39.8s, 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 384
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50047059
reads: 1001838
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.282 user 20.439 sys 21.822 real
done: 1 calls 0.004 user 0.000 sys 0.012 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.001 user 0.001 sys 1.975 real
idle: 83 calls 0.003 user 0.012 sys 47.247 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 166879232 mem 4.637 user 40.504 sys 3.546 real