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/aa/52e1eec3293dd7ed5a68037e2ebfc0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/115b64305d060833379ba5675af81f/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/aa/52e1eec3293dd7ed5a68037e2ebfc0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/115b64305d060833379ba5675af81f/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% @chr1:119000001, elapsed 0.0s, est remaining 0.5s, peak mem 108MB, user 0.1s, sys 0.4s, output queue size 42
progress 10% @chr2:59000001, elapsed 0.0s, est remaining 0.4s, peak mem 108MB, user 0.2s, sys 0.9s, output queue size 25
progress 15% @chr2:237000001, elapsed 0.1s, est remaining 0.4s, peak mem 108MB, user 0.3s, sys 1.5s, output queue size 21
progress 20% @chr3:157000001, elapsed 0.1s, est remaining 0.4s, peak mem 108MB, user 0.5s, sys 2.0s, output queue size 17
progress 25% @chr4:121000001, elapsed 0.1s, est remaining 0.3s, peak mem 108MB, user 0.5s, sys 2.5s, output queue size 32
progress 30% @chr5:88000001, elapsed 0.1s, est remaining 0.3s, peak mem 108MB, user 0.7s, sys 3.0s, output queue size 42
progress 35% @chr6:67000001, elapsed 0.2s, est remaining 0.3s, peak mem 108MB, user 0.8s, sys 3.5s, output queue size 34
progress 40% @chr7:27000001, elapsed 0.2s, est remaining 0.3s, peak mem 108MB, user 0.8s, sys 4.0s, output queue size 39
progress 45% @chr8:58000001, elapsed 0.2s, est remaining 0.2s, peak mem 108MB, user 0.9s, sys 4.5s, output queue size 43
progress 50% @chr9:45000001, elapsed 0.2s, est remaining 0.2s, peak mem 108MB, user 1.0s, sys 5.2s, output queue size 46
progress 55% @chr10:98000001, elapsed 0.2s, est remaining 0.2s, peak mem 108MB, user 1.2s, sys 5.7s, output queue size 46
progress 60% @chr11:127000001, elapsed 0.3s, est remaining 0.2s, peak mem 108MB, user 1.2s, sys 6.2s, output queue size 8
progress 65% @chr13:14000001, elapsed 0.3s, est remaining 0.1s, peak mem 108MB, user 1.3s, sys 6.9s, output queue size 18
progress 70% @chr14:63000001, elapsed 0.3s, est remaining 0.1s, peak mem 108MB, user 1.4s, sys 7.4s, output queue size 15
progress 75% @chr15:92000001, elapsed 0.3s, est remaining 0.1s, peak mem 108MB, user 1.5s, sys 7.9s, output queue size 23
progress 80% @chr18:5000001, elapsed 0.3s, est remaining 0.1s, peak mem 108MB, user 1.6s, sys 8.4s, output queue size 27
progress 85% @chr20:25000001, elapsed 0.4s, est remaining 0.1s, peak mem 108MB, user 1.7s, sys 9.1s, output queue size 14
progress 90% @chrX:41000001, elapsed 0.4s, est remaining 0.0s, peak mem 123MB, user 2.1s, sys 9.4s, output queue size 114
progress 95% @chrY:41000001, elapsed 0.4s, est remaining 0.0s, peak mem 135MB, user 2.6s, sys 9.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.0s, est remaining 0.0s, peak mem 150MB, user 4.4s, sys 10.5s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50047057
reads: 1001838
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.223 user 5.501 sys 6.922 real
done: 1 calls 0.002 user 0.000 sys 0.008 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.004 user 0.002 sys 0.992 real
idle: 83 calls 0.018 user 0.031 sys 45.881 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 157372416 mem 4.904 user 11.208 sys 2.462 real