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/38/b5844cec2bd391b74bab3eaee2f585/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/345e07031641f3739ef1e8a6665ff2/1029_I9B-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_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/27/345e07031641f3739ef1e8a6665ff2/1029_I9B-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/b5844cec2bd391b74bab3eaee2f585/.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 1029_I9B-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 1029_I9B-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 5.8s, est remaining 111.1s, peak mem 3898MB, user 132.8s, sys 3.3s, output queue size 146
progress 10% @chr2:71000001, elapsed 10.6s, est remaining 95.2s, peak mem 5043MB, user 283.7s, sys 5.5s, output queue size 166
progress 15% @chr2:74000001, elapsed 16.5s, est remaining 93.5s, peak mem 8131MB, user 467.5s, sys 8.7s, output queue size 161
progress 20% @chr3:155000001, elapsed 21.2s, est remaining 84.8s, peak mem 8131MB, user 598.6s, sys 9.8s, output queue size 283
progress 25% @chr4:135000001, elapsed 25.0s, est remaining 75.0s, peak mem 8260MB, user 734.9s, sys 10.8s, output queue size 302
progress 30% @chr5:83000001, elapsed 28.1s, est remaining 65.6s, peak mem 8551MB, user 813.6s, sys 11.4s, output queue size 464
progress 35% @chr6:27000001, elapsed 33.3s, est remaining 61.8s, peak mem 9455MB, user 958.7s, sys 12.8s, output queue size 625
progress 40% @chr7:66000001, elapsed 39.2s, est remaining 58.8s, peak mem 10260MB, user 1128.5s, sys 13.9s, output queue size 197
progress 45% @chr8:54000001, elapsed 44.8s, est remaining 54.8s, peak mem 10311MB, user 1311.5s, sys 15.6s, output queue size 356
progress 50% @chr9:81000001, elapsed 49.1s, est remaining 49.1s, peak mem 10311MB, user 1435.2s, sys 16.4s, output queue size 366
progress 55% @chr10:99000001, elapsed 54.7s, est remaining 44.7s, peak mem 10419MB, user 1615.4s, sys 17.4s, output queue size 348
progress 60% @chr12:1000001, elapsed 60.6s, est remaining 40.4s, peak mem 10419MB, user 1792.8s, sys 18.6s, output queue size 510
progress 65% @chr12:123000001, elapsed 66.3s, est remaining 35.7s, peak mem 10454MB, user 1945.5s, sys 19.5s, output queue size 672
progress 70% @chr14:85000001, elapsed 69.7s, est remaining 29.9s, peak mem 10522MB, user 2061.0s, sys 20.2s, output queue size 833
progress 75% @chr16:42000001, elapsed 75.4s, est remaining 25.1s, peak mem 10561MB, user 2250.0s, sys 21.5s, output queue size 461
progress 80% @chr18:1, elapsed 84.3s, est remaining 21.1s, peak mem 10801MB, user 2490.3s, sys 22.9s, output queue size 623
progress 85% @chr20:9000001, elapsed 92.6s, est remaining 16.3s, peak mem 10831MB, user 2748.4s, sys 24.2s, output queue size 785
progress 90% @chrX:42000001, elapsed 99.5s, est remaining 11.1s, peak mem 11684MB, user 2973.2s, sys 25.8s, output queue size 513
progress 95% @chrY:53000001, elapsed 103.7s, est remaining 5.5s, peak mem 11684MB, user 3099.2s, sys 26.9s, output queue size 675
progress 100% @chrX:67000001, elapsed 114.4s, est remaining 0.0s, peak mem 11688MB, user 3256.1s, sys 27.7s, 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: 81150013433
reads: 1554117329
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1291.782 user 24.642 sys 1316.424 real
done: 1 calls 0.358 user 0.040 sys 0.398 real
exec_no_coor: 1 calls 0.016 user 0.000 sys 0.026 real
execute: 1 calls 0.007 user 0.002 sys 114.425 real
idle: 323 calls 0.169 user 0.001 sys 304.455 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 12256006144 mem 3258.387 user 28.227 sys 116.620 real