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/d4/661db0d201363e56e0b1c87c8b9065/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/e6fd1550c035ef242c1bb22caf4565/Sig_18_tissue.md.bam.bai
  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/d4/661db0d201363e56e0b1c87c8b9065/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/e6fd1550c035ef242c1bb22caf4565/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-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_tissue_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% @chr1:161000001, elapsed 0.0s, est remaining 0.7s, peak mem 111MB, user 0.2s, sys 0.6s, output queue size 17
progress 10% @chr2:71000001, elapsed 0.1s, est remaining 0.6s, peak mem 111MB, user 0.4s, sys 1.5s, output queue size 2
progress 15% @chr2:235000001, elapsed 0.1s, est remaining 0.6s, peak mem 111MB, user 0.5s, sys 2.4s, output queue size 3
progress 20% @chr3:140000001, elapsed 0.1s, est remaining 0.5s, peak mem 111MB, user 0.6s, sys 3.2s, output queue size 13
progress 25% @chr4:103000001, elapsed 0.2s, est remaining 0.5s, peak mem 111MB, user 0.9s, sys 3.9s, output queue size 12
progress 30% @chr5:85000001, elapsed 0.2s, est remaining 0.5s, peak mem 111MB, user 1.0s, sys 4.6s, output queue size 16
progress 35% @chr6:60000001, elapsed 0.2s, est remaining 0.4s, peak mem 111MB, user 1.2s, sys 5.3s, output queue size 5
progress 40% @chr7:46000001, elapsed 0.3s, est remaining 0.4s, peak mem 111MB, user 1.3s, sys 6.6s, output queue size 17
progress 45% @chr8:42000001, elapsed 0.4s, est remaining 0.4s, peak mem 111MB, user 1.4s, sys 9.1s, output queue size 15
progress 50% @chr9:64000001, elapsed 0.4s, est remaining 0.4s, peak mem 111MB, user 1.5s, sys 11.4s, output queue size 18
progress 55% @chr10:88000001, elapsed 0.5s, est remaining 0.4s, peak mem 111MB, user 1.6s, sys 13.9s, output queue size 19
progress 60% @chr12:1, elapsed 0.6s, est remaining 0.4s, peak mem 111MB, user 1.7s, sys 16.1s, output queue size 18
progress 65% @chr13:3000001, elapsed 0.7s, est remaining 0.4s, peak mem 111MB, user 1.8s, sys 18.3s, output queue size 35
progress 70% @chr14:71000001, elapsed 0.8s, est remaining 0.3s, peak mem 111MB, user 1.9s, sys 20.7s, output queue size 15
progress 75% @chr16:22000001, elapsed 0.8s, est remaining 0.3s, peak mem 111MB, user 2.0s, sys 23.0s, output queue size 32
progress 80% @chr18:6000001, elapsed 0.9s, est remaining 0.2s, peak mem 111MB, user 2.1s, sys 25.3s, output queue size 15
progress 85% @chr20:6000001, elapsed 1.0s, est remaining 0.2s, peak mem 111MB, user 2.3s, sys 27.4s, output queue size 16
progress 90% @chrX:43000001, elapsed 1.1s, est remaining 0.1s, peak mem 120MB, user 2.8s, sys 29.0s, output queue size 114
progress 95% @chrY:48000001, elapsed 1.2s, est remaining 0.1s, peak mem 126MB, user 3.3s, sys 31.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.8s, est remaining 0.0s, peak mem 141MB, user 4.8s, sys 34.2s, 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 384
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50047058
reads: 1001838
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.372 user 18.088 sys 18.917 real
done: 1 calls 0.003 user 0.000 sys 0.009 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.001 user 0.001 sys 1.836 real
idle: 80 calls 0.002 user 0.009 sys 47.605 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 147947520 mem 5.292 user 34.933 sys 3.322 real