Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/b49f7aab1dd6f9c1751eae04df949f/.command.sh
  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/a5/5bccf33822723695cc22b7376f2be6/1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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/79/b49f7aab1dd6f9c1751eae04df949f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/5bccf33822723695cc22b7376f2be6/1136_5L2-T1-TDNA-1_A23MHWWLT4_1.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 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.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 1136_5L2-T1-TDNA-1_A23MHWWLT4_1_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% @chr1:178000001, elapsed 4.1s, est remaining 78.0s, peak mem 2815MB, user 96.9s, sys 2.6s, output queue size 146
progress 10% @chr1:243000001, elapsed 7.5s, est remaining 67.3s, peak mem 3664MB, user 204.1s, sys 4.6s, output queue size 117
progress 15% @chr3:13000001, elapsed 11.3s, est remaining 63.9s, peak mem 6127MB, user 307.3s, sys 6.7s, output queue size 203
progress 20% @chr3:175000001, elapsed 14.2s, est remaining 57.0s, peak mem 6202MB, user 397.2s, sys 8.9s, output queue size 283
progress 25% @chr4:65000001, elapsed 16.7s, est remaining 50.0s, peak mem 6204MB, user 486.1s, sys 9.6s, output queue size 302
progress 30% @chr5:97000001, elapsed 18.7s, est remaining 43.6s, peak mem 6392MB, user 544.4s, sys 10.1s, output queue size 464
progress 35% @chr5:150000001, elapsed 21.5s, est remaining 40.0s, peak mem 6511MB, user 622.6s, sys 10.8s, output queue size 625
progress 40% @chr7:64000001, elapsed 25.1s, est remaining 37.7s, peak mem 7060MB, user 712.3s, sys 11.5s, output queue size 786
progress 45% @chr8:78000001, elapsed 28.8s, est remaining 35.2s, peak mem 7326MB, user 830.6s, sys 12.3s, output queue size 948
progress 50% @chr9:102000001, elapsed 32.0s, est remaining 32.0s, peak mem 7498MB, user 926.1s, sys 12.9s, output queue size 366
progress 55% @chr10:101000001, elapsed 36.0s, est remaining 29.4s, peak mem 7592MB, user 1047.4s, sys 13.9s, output queue size 527
progress 60% @chr12:1000001, elapsed 39.9s, est remaining 26.6s, peak mem 7603MB, user 1165.4s, sys 14.7s, output queue size 689
progress 65% @chr12:123000001, elapsed 44.4s, est remaining 23.9s, peak mem 7690MB, user 1295.7s, sys 15.6s, output queue size 672
progress 70% @chr14:86000001, elapsed 47.0s, est remaining 20.1s, peak mem 7690MB, user 1361.4s, sys 16.0s, output queue size 833
progress 75% @chr16:42000001, elapsed 51.4s, est remaining 17.1s, peak mem 7729MB, user 1501.3s, sys 17.0s, output queue size 995
progress 80% @chr18:27000001, elapsed 56.9s, est remaining 14.2s, peak mem 7743MB, user 1675.8s, sys 17.9s, output queue size 623
progress 85% @chr19:45000001, elapsed 62.5s, est remaining 11.0s, peak mem 7761MB, user 1843.6s, sys 18.9s, output queue size 785
progress 90% @chrX:34000001, elapsed 65.6s, est remaining 7.3s, peak mem 7762MB, user 1952.7s, sys 19.4s, output queue size 947
progress 95% @chrY:53000001, elapsed 67.5s, est remaining 3.6s, peak mem 7786MB, user 1999.0s, sys 19.7s, output queue size 1109
progress 100% @chr22:23000001, elapsed 72.2s, est remaining 0.0s, peak mem 7786MB, user 2109.8s, sys 20.4s, output queue size 3635
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 52593107263
reads: 1002659546
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 822.325 user 17.906 sys 842.257 real
done: 1 calls 0.269 user 0.020 sys 0.293 real
exec_no_coor: 1 calls 0.008 user 0.000 sys 0.013 real
execute: 1 calls 0.004 user 0.002 sys 72.207 real
idle: 183 calls 0.127 user 0.001 sys 146.133 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 8164831232 mem 2111.599 user 20.856 sys 74.118 real