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/2e/e1ade7637c93fed371f1e514afe049/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/367c535ff2f0c527efeb80b165cce4/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/2e/e1ade7637c93fed371f1e514afe049/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/367c535ff2f0c527efeb80b165cce4/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% @chr1:159000001, elapsed 0.0s, est remaining 0.9s, peak mem 114MB, user 0.1s, sys 0.9s, output queue size 2
progress 10% @chr2:71000001, elapsed 0.1s, est remaining 0.8s, peak mem 114MB, user 0.1s, sys 2.2s, output queue size 2
progress 15% @chr2:236000001, elapsed 0.1s, est remaining 0.7s, peak mem 114MB, user 0.1s, sys 3.4s, output queue size 9
progress 20% @chr3:154000001, elapsed 0.2s, est remaining 0.7s, peak mem 114MB, user 0.2s, sys 4.7s, output queue size 1
progress 25% @chr4:114000001, elapsed 0.2s, est remaining 0.6s, peak mem 114MB, user 0.2s, sys 5.9s, output queue size 4
progress 30% @chr5:85000001, elapsed 0.3s, est remaining 0.6s, peak mem 114MB, user 0.3s, sys 7.1s, output queue size 5
progress 35% @chr6:64000001, elapsed 0.3s, est remaining 0.5s, peak mem 114MB, user 0.3s, sys 8.3s, output queue size 1
progress 40% @chr7:56000001, elapsed 0.3s, est remaining 0.5s, peak mem 114MB, user 0.4s, sys 9.5s, output queue size 2
progress 45% @chr8:55000001, elapsed 0.4s, est remaining 0.5s, peak mem 114MB, user 0.4s, sys 10.7s, output queue size 4
progress 50% @chr9:71000001, elapsed 0.4s, est remaining 0.4s, peak mem 114MB, user 0.5s, sys 12.0s, output queue size 2
progress 55% @chr10:94000001, elapsed 0.5s, est remaining 0.4s, peak mem 114MB, user 0.6s, sys 13.2s, output queue size 6
progress 60% @chr11:121000001, elapsed 0.5s, est remaining 0.3s, peak mem 114MB, user 0.6s, sys 14.4s, output queue size 2
progress 65% @chr13:14000001, elapsed 0.5s, est remaining 0.3s, peak mem 114MB, user 0.6s, sys 15.6s, output queue size 1
progress 70% @chr14:62000001, elapsed 0.6s, est remaining 0.3s, peak mem 114MB, user 0.7s, sys 16.8s, output queue size 12
progress 75% @chr16:10000001, elapsed 0.6s, est remaining 0.2s, peak mem 114MB, user 0.8s, sys 18.0s, output queue size 3
progress 80% @chr18:3000001, elapsed 0.7s, est remaining 0.2s, peak mem 114MB, user 0.8s, sys 19.2s, output queue size 5
progress 85% @chr20:19000001, elapsed 0.7s, est remaining 0.1s, peak mem 114MB, user 0.9s, sys 20.4s, output queue size 8
progress 90% @chrX:39000001, elapsed 0.8s, est remaining 0.1s, peak mem 147MB, user 1.2s, sys 21.2s, output queue size 114
progress 95% @chrY:35000001, elapsed 0.8s, est remaining 0.0s, peak mem 159MB, user 1.7s, sys 22.0s, output queue size 271
progress 100% @chr21:41000001, elapsed 1.2s, est remaining 0.0s, peak mem 172MB, user 3.0s, sys 23.3s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 50044781
reads: 1001838
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.151 user 11.562 sys 13.307 real
done: 1 calls 0.006 user 0.000 sys 0.009 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.002 sys 1.160 real
idle: 75 calls 0.006 user 0.026 sys 39.602 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 181166080 mem 3.333 user 24.026 sys 2.602 real