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/a1/2c4c8e0486ec18df175cad145a1803/.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/1d/a3bfa4f3b7b844a1d75cbc0e235b9e/1136_5KC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/2c4c8e0486ec18df175cad145a1803/.command.run
  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/1d/a3bfa4f3b7b844a1d75cbc0e235b9e/1136_5KC-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.bed
==> STAGING COMPLETE (8 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 1136_5KC-T1-TDNA-1_A23MHWWLT4_1.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 1136_5KC-T1-TDNA-1_A23MHWWLT4_1_foresight_clarity_targets_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 3.2s, est remaining 60.3s, peak mem 2746MB, user 70.6s, sys 2.1s, output queue size 150
progress 10% @chr2:94000001, elapsed 5.7s, est remaining 51.7s, peak mem 3481MB, user 155.1s, sys 3.6s, output queue size 117
progress 15% @chr2:201000001, elapsed 8.4s, est remaining 47.7s, peak mem 4925MB, user 234.2s, sys 5.4s, output queue size 203
progress 20% @chr3:174000001, elapsed 10.6s, est remaining 42.5s, peak mem 4993MB, user 302.5s, sys 7.0s, output queue size 283
progress 25% @chr4:124000001, elapsed 12.6s, est remaining 37.8s, peak mem 5044MB, user 363.8s, sys 7.8s, output queue size 302
progress 30% @chr5:94000001, elapsed 14.1s, est remaining 32.9s, peak mem 5183MB, user 405.9s, sys 8.4s, output queue size 464
progress 35% @chr6:56000001, elapsed 16.4s, est remaining 30.5s, peak mem 5250MB, user 469.3s, sys 9.0s, output queue size 625
progress 40% @chr7:66000001, elapsed 19.0s, est remaining 28.5s, peak mem 5636MB, user 538.3s, sys 9.6s, output queue size 786
progress 45% @chr8:78000001, elapsed 21.8s, est remaining 26.6s, peak mem 5898MB, user 638.3s, sys 10.7s, output queue size 204
progress 50% @chr9:88000001, elapsed 24.0s, est remaining 24.0s, peak mem 5991MB, user 700.8s, sys 11.3s, output queue size 366
progress 55% @chr10:99000001, elapsed 26.9s, est remaining 22.0s, peak mem 6133MB, user 789.2s, sys 12.2s, output queue size 348
progress 60% @chr12:5000001, elapsed 29.7s, est remaining 19.8s, peak mem 6133MB, user 869.4s, sys 12.7s, output queue size 510
progress 65% @chr13:33000001, elapsed 32.5s, est remaining 17.5s, peak mem 6274MB, user 953.1s, sys 13.5s, output queue size 672
progress 70% @chr14:85000001, elapsed 34.2s, est remaining 14.6s, peak mem 6306MB, user 998.7s, sys 13.8s, output queue size 833
progress 75% @chr16:42000001, elapsed 37.3s, est remaining 12.4s, peak mem 6306MB, user 1106.3s, sys 14.5s, output queue size 461
progress 80% @chr18:9000001, elapsed 41.7s, est remaining 10.4s, peak mem 6339MB, user 1227.5s, sys 15.5s, output queue size 623
progress 85% @chr19:55000001, elapsed 45.9s, est remaining 8.1s, peak mem 6373MB, user 1362.1s, sys 16.5s, output queue size 785
progress 90% @chrX:34000001, elapsed 48.5s, est remaining 5.4s, peak mem 6389MB, user 1455.7s, sys 17.2s, output queue size 513
progress 95% @chrY:54000001, elapsed 50.5s, est remaining 2.7s, peak mem 6478MB, user 1502.2s, sys 17.6s, output queue size 675
progress 100% @chrX:67000001, elapsed 56.3s, est remaining 0.0s, peak mem 6478MB, user 1590.6s, sys 18.2s, 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: 50938789543
reads: 986308211
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 782.469 user 15.488 sys 799.094 real
done: 1 calls 0.005 user 0.009 sys 0.017 real
exec_no_coor: 1 calls 0.004 user 0.000 sys 0.005 real
execute: 1 calls 0.002 user 0.000 sys 56.285 real
idle: 173 calls 0.146 user 0.001 sys 165.359 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 6793474048 mem 1591.434 user 18.344 sys 57.515 real