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/92/ee5b224013d0a88338be0c2ae81429/.command.sh
  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/92/ee5b224013d0a88338be0c2ae81429/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/115b07df53c7e3fa9b92ccd72628ba/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/115b07df53c7e3fa9b92ccd72628ba/Sig_18_Blood.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.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_Blood.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_Blood_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% @chr1:160000001, elapsed 0.1s, est remaining 1.3s, peak mem 105MB, user 0.0s, sys 0.1s, output queue size 1
progress 10% @chr2:72000001, elapsed 0.1s, est remaining 1.3s, peak mem 105MB, user 0.0s, sys 0.1s, output queue size 1
progress 15% @chr2:233000001, elapsed 0.2s, est remaining 1.2s, peak mem 105MB, user 0.0s, sys 0.1s, output queue size 1
progress 20% @chr3:152000001, elapsed 0.3s, est remaining 1.2s, peak mem 105MB, user 0.1s, sys 0.2s, output queue size 1
progress 25% @chr4:114000001, elapsed 0.4s, est remaining 1.1s, peak mem 105MB, user 0.1s, sys 0.2s, output queue size 1
progress 30% @chr5:85000001, elapsed 0.4s, est remaining 1.0s, peak mem 105MB, user 0.1s, sys 0.2s, output queue size 1
progress 35% @chr6:64000001, elapsed 0.5s, est remaining 0.9s, peak mem 105MB, user 0.2s, sys 0.3s, output queue size 1
progress 40% @chr7:54000001, elapsed 0.6s, est remaining 0.8s, peak mem 105MB, user 0.2s, sys 0.3s, output queue size 1
progress 45% @chr8:56000001, elapsed 0.6s, est remaining 0.8s, peak mem 105MB, user 0.3s, sys 0.3s, output queue size 1
progress 50% @chr9:72000001, elapsed 0.7s, est remaining 0.7s, peak mem 105MB, user 0.3s, sys 0.3s, output queue size 1
progress 55% @chr10:94000001, elapsed 0.8s, est remaining 0.6s, peak mem 105MB, user 0.3s, sys 0.4s, output queue size 1
progress 60% @chr11:121000001, elapsed 0.8s, est remaining 0.5s, peak mem 105MB, user 0.3s, sys 0.4s, output queue size 1
progress 65% @chr13:14000001, elapsed 0.9s, est remaining 0.5s, peak mem 105MB, user 0.4s, sys 0.5s, output queue size 1
progress 70% @chr14:60000001, elapsed 1.0s, est remaining 0.4s, peak mem 105MB, user 0.4s, sys 0.5s, output queue size 1
progress 75% @chr16:12000001, elapsed 1.0s, est remaining 0.3s, peak mem 105MB, user 0.4s, sys 0.5s, output queue size 1
progress 80% @chr17:76000001, elapsed 1.1s, est remaining 0.3s, peak mem 105MB, user 0.5s, sys 1.8s, output queue size 33
progress 85% @chr20:13000001, elapsed 1.1s, est remaining 0.2s, peak mem 105MB, user 0.6s, sys 3.7s, output queue size 9
progress 90% @chrX:34000001, elapsed 1.2s, est remaining 0.1s, peak mem 120MB, user 1.1s, sys 4.7s, output queue size 114
progress 95% @chrY:29000001, elapsed 1.3s, est remaining 0.1s, peak mem 132MB, user 1.7s, sys 6.1s, output queue size 271
progress 100% @chr21:41000001, elapsed 1.9s, est remaining 0.0s, peak mem 153MB, user 3.2s, sys 8.1s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 52290594
reads: 1001133
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.049 user 4.512 sys 5.784 real
done: 1 calls 0.005 user 0.006 sys 0.018 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.004 sys 1.901 real
idle: 62 calls 0.009 user 0.017 sys 46.739 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 160571392 mem 3.701 user 8.790 sys 3.586 real