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/32/66ab7d6c368b31ed5e5c3102ff15f4/.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/71/81816b54ab7484624d9fee8b6881d3/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/66ab7d6c368b31ed5e5c3102ff15f4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/81816b54ab7484624d9fee8b6881d3/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% @chr1:162000001, elapsed 0.1s, est remaining 1.0s, peak mem 114MB, user 0.0s, sys 1.2s, output queue size 6
progress 10% @chr2:74000001, elapsed 0.1s, est remaining 0.9s, peak mem 114MB, user 0.1s, sys 2.5s, output queue size 41
progress 15% @chr3:18000001, elapsed 0.1s, est remaining 0.8s, peak mem 114MB, user 0.1s, sys 4.0s, output queue size 7
progress 20% @chr3:178000001, elapsed 0.2s, est remaining 0.8s, peak mem 114MB, user 0.2s, sys 5.5s, output queue size 10
progress 25% @chr4:107000001, elapsed 0.3s, est remaining 0.8s, peak mem 114MB, user 0.3s, sys 7.0s, output queue size 8
progress 30% @chr5:83000001, elapsed 0.3s, est remaining 0.7s, peak mem 114MB, user 0.5s, sys 8.4s, output queue size 18
progress 35% @chr6:57000001, elapsed 0.4s, est remaining 0.7s, peak mem 114MB, user 0.6s, sys 9.9s, output queue size 8
progress 40% @chr7:49000001, elapsed 0.4s, est remaining 0.6s, peak mem 114MB, user 0.6s, sys 11.4s, output queue size 7
progress 45% @chr8:54000001, elapsed 0.5s, est remaining 0.6s, peak mem 114MB, user 0.7s, sys 13.0s, output queue size 11
progress 50% @chr9:66000001, elapsed 0.5s, est remaining 0.5s, peak mem 114MB, user 0.8s, sys 14.5s, output queue size 7
progress 55% @chr10:122000001, elapsed 0.6s, est remaining 0.5s, peak mem 114MB, user 0.9s, sys 15.9s, output queue size 7
progress 60% @chr11:113000001, elapsed 0.6s, est remaining 0.4s, peak mem 114MB, user 1.0s, sys 17.3s, output queue size 10
progress 65% @chr13:37000001, elapsed 0.7s, est remaining 0.4s, peak mem 114MB, user 1.1s, sys 18.7s, output queue size 6
progress 70% @chr14:54000001, elapsed 0.7s, est remaining 0.3s, peak mem 114MB, user 1.2s, sys 20.2s, output queue size 8
progress 75% @chr16:9000001, elapsed 0.8s, est remaining 0.3s, peak mem 114MB, user 1.3s, sys 21.6s, output queue size 8
progress 80% @chr18:25000001, elapsed 0.8s, est remaining 0.2s, peak mem 114MB, user 1.3s, sys 23.1s, output queue size 9
progress 85% @chr20:14000001, elapsed 0.9s, est remaining 0.2s, peak mem 114MB, user 1.4s, sys 24.6s, output queue size 9
progress 90% @chrX:36000001, elapsed 0.9s, est remaining 0.1s, peak mem 129MB, user 1.9s, sys 25.8s, output queue size 114
progress 95% @chrY:32000001, elapsed 1.0s, est remaining 0.1s, peak mem 144MB, user 2.3s, sys 26.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.6s, est remaining 0.0s, peak mem 165MB, user 3.9s, sys 28.9s, 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: 51395350
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.340 user 14.605 sys 16.442 real
done: 1 calls 0.004 user 0.000 sys 0.012 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.002 sys 1.589 real
idle: 81 calls 0.003 user 0.012 sys 46.410 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 173154304 mem 4.435 user 29.588 sys 3.126 real