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/d8/9a7e14e27042e576900f5c2db0d4ff/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/b1e9f54065543beb31deeb373b4c5d/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-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_postQC_hg38.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/9a7e14e27042e576900f5c2db0d4ff/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/b1e9f54065543beb31deeb373b4c5d/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/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_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 0.0s, est remaining 0.6s, peak mem 99MB, user 0.0s, sys 0.7s, output queue size 1
progress 10% @chr2:73000001, elapsed 0.1s, est remaining 0.5s, peak mem 99MB, user 0.1s, sys 1.4s, output queue size 24
progress 15% @chr2:237000001, elapsed 0.1s, est remaining 0.5s, peak mem 99MB, user 0.2s, sys 2.1s, output queue size 24
progress 20% @chr3:143000001, elapsed 0.1s, est remaining 0.5s, peak mem 99MB, user 0.3s, sys 2.9s, output queue size 26
progress 25% @chr4:112000001, elapsed 0.1s, est remaining 0.4s, peak mem 99MB, user 0.4s, sys 3.7s, output queue size 13
progress 30% @chr5:85000001, elapsed 0.2s, est remaining 0.4s, peak mem 99MB, user 0.4s, sys 4.5s, output queue size 5
progress 35% @chr6:68000001, elapsed 0.2s, est remaining 0.4s, peak mem 99MB, user 0.5s, sys 5.3s, output queue size 15
progress 40% @chr7:55000001, elapsed 0.2s, est remaining 0.3s, peak mem 99MB, user 0.6s, sys 6.0s, output queue size 22
progress 45% @chr8:49000001, elapsed 0.3s, est remaining 0.3s, peak mem 99MB, user 0.6s, sys 6.8s, output queue size 8
progress 50% @chr9:74000001, elapsed 0.3s, est remaining 0.3s, peak mem 99MB, user 0.6s, sys 7.7s, output queue size 3
progress 55% @chr10:94000001, elapsed 0.3s, est remaining 0.3s, peak mem 99MB, user 0.7s, sys 8.6s, output queue size 21
progress 60% @chr11:121000001, elapsed 0.3s, est remaining 0.2s, peak mem 99MB, user 0.8s, sys 9.5s, output queue size 3
progress 65% @chr13:19000001, elapsed 0.4s, est remaining 0.2s, peak mem 99MB, user 0.9s, sys 10.4s, output queue size 17
progress 70% @chr14:57000001, elapsed 0.4s, est remaining 0.2s, peak mem 99MB, user 1.0s, sys 11.3s, output queue size 8
progress 75% @chr16:17000001, elapsed 0.4s, est remaining 0.1s, peak mem 99MB, user 1.1s, sys 12.1s, output queue size 3
progress 80% @chr18:4000001, elapsed 0.5s, est remaining 0.1s, peak mem 99MB, user 1.2s, sys 13.0s, output queue size 15
progress 85% @chr20:23000001, elapsed 0.5s, est remaining 0.1s, peak mem 99MB, user 1.4s, sys 14.0s, output queue size 17
progress 90% @chrX:38000001, elapsed 0.6s, est remaining 0.1s, peak mem 114MB, user 1.9s, sys 14.6s, output queue size 114
progress 95% @chrY:34000001, elapsed 0.6s, est remaining 0.0s, peak mem 126MB, user 2.3s, sys 15.4s, output queue size 271
progress 100% @chr21:41000001, elapsed 1.1s, est remaining 0.0s, peak mem 141MB, user 3.5s, sys 16.5s, 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 1.273 user 8.759 sys 9.904 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.002 sys 1.158 real
idle: 82 calls 0.008 user 0.017 sys 45.699 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 148004864 mem 3.747 user 17.174 sys 2.322 real