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/a1/ac00e0916438cf08e3f0c43ccb4913/.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/9b/f549beb0103827e9d5cda373213fce/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/ac00e0916438cf08e3f0c43ccb4913/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/f549beb0103827e9d5cda373213fce/HCC1395_BL.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 HCC1395_BL.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 HCC1395_BL_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% @chr1:157000001, elapsed 0.0s, est remaining 0.4s, peak mem 118MB, user 0.1s, sys 0.3s, output queue size 28
progress 10% @chr2:68000001, elapsed 0.0s, est remaining 0.4s, peak mem 118MB, user 0.2s, sys 0.8s, output queue size 6
progress 15% @chr3:7000001, elapsed 0.1s, est remaining 0.4s, peak mem 118MB, user 0.3s, sys 1.3s, output queue size 4
progress 20% @chr3:170000001, elapsed 0.1s, est remaining 0.3s, peak mem 118MB, user 0.4s, sys 1.9s, output queue size 17
progress 25% @chr4:131000001, elapsed 0.1s, est remaining 0.3s, peak mem 118MB, user 0.4s, sys 2.4s, output queue size 3
progress 30% @chr5:101000001, elapsed 0.1s, est remaining 0.3s, peak mem 118MB, user 0.5s, sys 3.0s, output queue size 25
progress 35% @chr6:64000001, elapsed 0.1s, est remaining 0.3s, peak mem 118MB, user 0.6s, sys 3.5s, output queue size 20
progress 40% @chr7:53000001, elapsed 0.2s, est remaining 0.3s, peak mem 118MB, user 0.6s, sys 4.1s, output queue size 25
progress 45% @chr8:55000001, elapsed 0.2s, est remaining 0.2s, peak mem 118MB, user 0.7s, sys 4.6s, output queue size 5
progress 50% @chr9:70000001, elapsed 0.2s, est remaining 0.2s, peak mem 118MB, user 0.8s, sys 5.2s, output queue size 28
progress 55% @chr10:90000001, elapsed 0.2s, est remaining 0.2s, peak mem 118MB, user 0.9s, sys 5.8s, output queue size 5
progress 60% @chr11:118000001, elapsed 0.3s, est remaining 0.2s, peak mem 118MB, user 1.0s, sys 6.3s, output queue size 6
progress 65% @chr13:10000001, elapsed 0.3s, est remaining 0.1s, peak mem 118MB, user 1.0s, sys 6.9s, output queue size 17
progress 70% @chr14:58000001, elapsed 0.3s, est remaining 0.1s, peak mem 118MB, user 1.2s, sys 7.4s, output queue size 8
progress 75% @chr16:8000001, elapsed 0.3s, est remaining 0.1s, peak mem 118MB, user 1.4s, sys 7.8s, output queue size 5
progress 80% @chr17:80000001, elapsed 0.3s, est remaining 0.1s, peak mem 118MB, user 1.5s, sys 8.3s, output queue size 8
progress 85% @chr20:19000001, elapsed 0.4s, est remaining 0.1s, peak mem 118MB, user 1.6s, sys 8.8s, output queue size 27
progress 90% @chr21:40000001, elapsed 0.4s, est remaining 0.0s, peak mem 141MB, user 1.9s, sys 9.1s, output queue size 114
progress 95% @chrY:39000001, elapsed 0.4s, est remaining 0.0s, peak mem 163MB, user 2.3s, sys 9.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 0.9s, est remaining 0.0s, peak mem 184MB, user 4.2s, sys 9.8s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 51395351
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.154 user 4.671 sys 6.405 real
done: 1 calls 0.003 user 0.000 sys 0.008 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.001 sys 0.935 real
idle: 82 calls 0.022 user 0.039 sys 45.160 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 195321856 mem 4.774 user 10.446 sys 2.519 real