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/2d/1bc866655a87b3060b42cc0adb413c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/e2109afe678e2520271a463d7be2f0/659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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/69/e2109afe678e2520271a463d7be2f0/659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/1bc866655a87b3060b42cc0adb413c/.command.run
  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 659_cfy-T1-TDNA-1_A23MHWWLT4_1.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 659_cfy-T1-TDNA-1_A23MHWWLT4_1_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% @chr1:187000001, elapsed 5.9s, est remaining 112.4s, peak mem 3671MB, user 136.7s, sys 3.1s, output queue size 146
progress 10% @chr2:42000001, elapsed 10.7s, est remaining 96.0s, peak mem 4823MB, user 288.7s, sys 6.2s, output queue size 117
progress 15% @chr3:18000001, elapsed 16.2s, est remaining 92.0s, peak mem 6948MB, user 443.9s, sys 12.8s, output queue size 188
progress 20% @chr3:175000001, elapsed 20.7s, est remaining 82.6s, peak mem 7183MB, user 588.7s, sys 14.4s, output queue size 174
progress 25% @chr4:133000001, elapsed 24.7s, est remaining 74.0s, peak mem 7387MB, user 713.0s, sys 15.6s, output queue size 302
progress 30% @chr5:83000001, elapsed 27.8s, est remaining 64.9s, peak mem 7660MB, user 806.9s, sys 16.2s, output queue size 464
progress 35% @chr6:52000001, elapsed 32.4s, est remaining 60.1s, peak mem 7798MB, user 928.9s, sys 17.1s, output queue size 625
progress 40% @chr6:152000001, elapsed 36.8s, est remaining 55.3s, peak mem 7958MB, user 1057.5s, sys 17.9s, output queue size 786
progress 45% @chr8:83000001, elapsed 42.6s, est remaining 52.1s, peak mem 8251MB, user 1216.4s, sys 18.7s, output queue size 948
progress 50% @chr9:87000001, elapsed 46.6s, est remaining 46.6s, peak mem 8332MB, user 1353.0s, sys 19.6s, output queue size 366
progress 55% @chr10:104000001, elapsed 51.3s, est remaining 42.0s, peak mem 8332MB, user 1500.4s, sys 20.6s, output queue size 527
progress 60% @chr11:130000001, elapsed 56.7s, est remaining 37.8s, peak mem 8332MB, user 1659.9s, sys 21.5s, output queue size 510
progress 65% @chr12:102000001, elapsed 62.4s, est remaining 33.6s, peak mem 8332MB, user 1836.8s, sys 22.5s, output queue size 672
progress 70% @chr14:35000001, elapsed 65.7s, est remaining 28.2s, peak mem 8352MB, user 1937.7s, sys 23.3s, output queue size 833
progress 75% @chr16:42000001, elapsed 72.2s, est remaining 24.1s, peak mem 8545MB, user 2105.8s, sys 24.3s, output queue size 995
progress 80% @chr17:78000001, elapsed 81.1s, est remaining 20.3s, peak mem 8734MB, user 2385.0s, sys 25.9s, output queue size 623
progress 85% @chr19:55000001, elapsed 89.2s, est remaining 15.7s, peak mem 8781MB, user 2675.8s, sys 27.4s, output queue size 351
progress 90% @chrX:30000001, elapsed 94.4s, est remaining 10.5s, peak mem 8998MB, user 2835.0s, sys 28.4s, output queue size 513
progress 95% @chrY:53000001, elapsed 98.0s, est remaining 5.2s, peak mem 8998MB, user 2955.6s, sys 29.1s, output queue size 240
progress 100% @chrX:67000001, elapsed 108.6s, est remaining 0.0s, peak mem 9017MB, user 3079.8s, sys 30.1s, output queue size 3540
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: 69852823730
reads: 1410512872
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1123.036 user 26.704 sys 1150.936 real
done: 1 calls 0.288 user 0.089 sys 0.386 real
exec_no_coor: 1 calls 0.014 user 0.000 sys 0.029 real
execute: 1 calls 0.002 user 0.001 sys 108.671 real
idle: 327 calls 0.171 user 0.011 sys 295.341 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 9456033792 mem 3081.890 user 30.657 sys 110.692 real