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/14/78cfe0675ab1c5bab1a6d659c9aee1/.command.sh
  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/14/78cfe0675ab1c5bab1a6d659c9aee1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/1522110040efeb211ec882b01ba433/Sig_18_Blood.md.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/foresight_clarity_targets_hg38.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/1522110040efeb211ec882b01ba433/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/foresight_clarity_targets_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_Blood_foresight_clarity_targets_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:161000001, elapsed 0.0s, est remaining 0.4s, peak mem 100MB, user 0.0s, sys 0.3s, output queue size 3
progress 10% @chr2:71000001, elapsed 0.0s, est remaining 0.3s, peak mem 100MB, user 0.1s, sys 0.7s, output queue size 2
progress 15% @chr2:233000001, elapsed 0.1s, est remaining 0.3s, peak mem 100MB, user 0.2s, sys 1.1s, output queue size 2
progress 20% @chr3:153000001, elapsed 0.1s, est remaining 0.3s, peak mem 100MB, user 0.2s, sys 1.6s, output queue size 1
progress 25% @chr4:115000001, elapsed 0.1s, est remaining 0.3s, peak mem 100MB, user 0.3s, sys 2.1s, output queue size 1
progress 30% @chr5:86000001, elapsed 0.1s, est remaining 0.3s, peak mem 100MB, user 0.4s, sys 2.7s, output queue size 1
progress 35% @chr6:66000001, elapsed 0.1s, est remaining 0.2s, peak mem 100MB, user 0.4s, sys 3.0s, output queue size 2
progress 40% @chr7:53000001, elapsed 0.1s, est remaining 0.2s, peak mem 100MB, user 0.4s, sys 3.5s, output queue size 2
progress 45% @chr8:56000001, elapsed 0.2s, est remaining 0.2s, peak mem 100MB, user 0.5s, sys 4.0s, output queue size 1
progress 50% @chr9:75000001, elapsed 0.2s, est remaining 0.2s, peak mem 100MB, user 0.5s, sys 4.5s, output queue size 3
progress 55% @chr10:93000001, elapsed 0.2s, est remaining 0.2s, peak mem 100MB, user 0.6s, sys 5.0s, output queue size 4
progress 60% @chr11:119000001, elapsed 0.2s, est remaining 0.1s, peak mem 100MB, user 0.6s, sys 5.4s, output queue size 4
progress 65% @chr13:14000001, elapsed 0.2s, est remaining 0.1s, peak mem 100MB, user 0.7s, sys 5.9s, output queue size 1
progress 70% @chr14:59000001, elapsed 0.3s, est remaining 0.1s, peak mem 100MB, user 0.8s, sys 6.4s, output queue size 2
progress 75% @chr16:13000001, elapsed 0.3s, est remaining 0.1s, peak mem 100MB, user 0.8s, sys 6.9s, output queue size 2
progress 80% @chr18:1, elapsed 0.3s, est remaining 0.1s, peak mem 100MB, user 0.9s, sys 7.2s, output queue size 2
progress 85% @chr20:21000001, elapsed 0.3s, est remaining 0.1s, peak mem 100MB, user 1.0s, sys 7.7s, output queue size 1
progress 90% @chrX:40000001, elapsed 0.3s, est remaining 0.0s, peak mem 129MB, user 1.3s, sys 8.0s, output queue size 114
progress 95% @chrY:38000001, elapsed 0.4s, est remaining 0.0s, peak mem 144MB, user 1.6s, sys 8.5s, output queue size 276
progress 100% @chr21:41000001, elapsed 0.7s, est remaining 0.0s, peak mem 162MB, user 3.0s, sys 8.9s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 52290599
reads: 1001133
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.434 user 4.392 sys 6.208 real
done: 1 calls 0.000 user 0.000 sys 0.001 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.004 user 0.001 sys 0.717 real
idle: 79 calls 0.010 user 0.021 sys 40.332 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 171728896 mem 3.310 user 9.551 sys 1.883 real