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/f7/2c3523a4291fb2824e921f6f5c306d/.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/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/f7/2c3523a4291fb2824e921f6f5c306d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_noncoding_postQC_hg38.bed
  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/altera_v3_targets_noncoding_postQC_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 659_cfy-T1-TDNA-1_A23MHWWLT4_1_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 4.7s, est remaining 88.6s, peak mem 3992MB, user 111.7s, sys 3.6s, output queue size 146
progress 10% @chr2:27000001, elapsed 8.3s, est remaining 75.1s, peak mem 5035MB, user 225.0s, sys 6.0s, output queue size 117
progress 15% @chr3:4000001, elapsed 12.7s, est remaining 71.9s, peak mem 6919MB, user 350.0s, sys 9.0s, output queue size 188
progress 20% @chr3:158000001, elapsed 16.2s, est remaining 64.9s, peak mem 6984MB, user 455.0s, sys 10.4s, output queue size 283
progress 25% @chr4:134000001, elapsed 19.4s, est remaining 58.2s, peak mem 7253MB, user 560.4s, sys 11.5s, output queue size 302
progress 30% @chr5:107000001, elapsed 21.9s, est remaining 51.0s, peak mem 7447MB, user 634.0s, sys 12.1s, output queue size 464
progress 35% @chr5:141000001, elapsed 25.3s, est remaining 47.1s, peak mem 7577MB, user 731.5s, sys 13.5s, output queue size 625
progress 40% @chr7:66000001, elapsed 28.8s, est remaining 43.2s, peak mem 7712MB, user 823.6s, sys 14.2s, output queue size 786
progress 45% @chr8:78000001, elapsed 33.1s, est remaining 40.5s, peak mem 8000MB, user 943.5s, sys 15.3s, output queue size 948
progress 50% @chr9:35000001, elapsed 36.3s, est remaining 36.3s, peak mem 8125MB, user 1027.4s, sys 15.9s, output queue size 1110
progress 55% @chr10:115000001, elapsed 39.9s, est remaining 32.7s, peak mem 8129MB, user 1157.5s, sys 17.0s, output queue size 527
progress 60% @chr11:134000001, elapsed 43.7s, est remaining 29.2s, peak mem 8169MB, user 1269.5s, sys 17.6s, output queue size 689
progress 65% @chr12:111000001, elapsed 48.3s, est remaining 26.0s, peak mem 8242MB, user 1396.0s, sys 18.6s, output queue size 851
progress 70% @chr13:102000001, elapsed 50.9s, est remaining 21.8s, peak mem 8242MB, user 1505.2s, sys 19.2s, output queue size 833
progress 75% @chr16:42000001, elapsed 55.5s, est remaining 18.5s, peak mem 8243MB, user 1624.5s, sys 20.0s, output queue size 995
progress 80% @chr18:25000001, elapsed 62.0s, est remaining 15.5s, peak mem 8377MB, user 1793.9s, sys 21.3s, output queue size 1157
progress 85% @chr20:23000001, elapsed 68.1s, est remaining 12.0s, peak mem 8434MB, user 1976.6s, sys 22.4s, output queue size 1319
progress 90% @chrX:30000001, elapsed 72.0s, est remaining 8.0s, peak mem 8631MB, user 2133.4s, sys 23.2s, output queue size 947
progress 95% @chrY:53000001, elapsed 74.8s, est remaining 3.9s, peak mem 8700MB, user 2231.2s, sys 23.9s, output queue size 675
progress 100% @chrX:67000001, elapsed 84.9s, est remaining 0.0s, peak mem 8700MB, user 2364.8s, sys 24.9s, output queue size 3540
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 69852823730
reads: 1410512872
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1106.949 user 21.757 sys 1133.285 real
done: 1 calls 0.016 user 0.008 sys 0.032 real
exec_no_coor: 1 calls 0.012 user 0.006 sys 0.034 real
execute: 1 calls 0.002 user 0.001 sys 84.945 real
idle: 299 calls 0.118 user 0.001 sys 272.750 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 9122955264 mem 2365.603 user 25.086 sys 86.237 real