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/22/72eb9e3644f71022ac35d8eb3b9290/.command.sh
  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/10/80d1b6be657723bff7162ae1f1c74e/659_eKx-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/80d1b6be657723bff7162ae1f1c74e/659_eKx-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/72eb9e3644f71022ac35d8eb3b9290/.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_eKx-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 659_eKx-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% @chr1:163000001, elapsed 0.0s, est remaining 0.5s, peak mem 117MB, user 0.2s, sys 0.2s, output queue size 9
progress 10% @chr2:71000001, elapsed 0.0s, est remaining 0.4s, peak mem 118MB, user 0.2s, sys 0.8s, output queue size 41
progress 15% @chr2:231000001, elapsed 0.1s, est remaining 0.4s, peak mem 123MB, user 0.3s, sys 1.4s, output queue size 203
progress 20% @chr3:149000001, elapsed 0.1s, est remaining 0.4s, peak mem 127MB, user 0.4s, sys 2.1s, output queue size 364
progress 25% @chr4:111000001, elapsed 0.1s, est remaining 0.4s, peak mem 130MB, user 0.4s, sys 2.7s, output queue size 525
progress 30% @chr5:101000001, elapsed 0.1s, est remaining 0.3s, peak mem 135MB, user 0.6s, sys 3.4s, output queue size 115
progress 35% @chr6:61000001, elapsed 0.2s, est remaining 0.3s, peak mem 136MB, user 0.7s, sys 4.0s, output queue size 4
progress 40% @chr7:48000001, elapsed 0.2s, est remaining 0.3s, peak mem 138MB, user 0.8s, sys 4.5s, output queue size 7
progress 45% @chr8:54000001, elapsed 0.2s, est remaining 0.3s, peak mem 139MB, user 0.9s, sys 5.0s, output queue size 25
progress 50% @chr9:68000001, elapsed 0.2s, est remaining 0.2s, peak mem 141MB, user 0.9s, sys 5.6s, output queue size 5
progress 55% @chr10:113000001, elapsed 0.3s, est remaining 0.2s, peak mem 142MB, user 1.1s, sys 6.1s, output queue size 4
progress 60% @chr11:117000001, elapsed 0.3s, est remaining 0.2s, peak mem 144MB, user 1.2s, sys 6.7s, output queue size 6
progress 65% @chr13:10000001, elapsed 0.3s, est remaining 0.2s, peak mem 145MB, user 1.3s, sys 7.2s, output queue size 7
progress 70% @chr14:59000001, elapsed 0.3s, est remaining 0.1s, peak mem 145MB, user 1.4s, sys 7.8s, output queue size 7
progress 75% @chr16:13000001, elapsed 0.3s, est remaining 0.1s, peak mem 147MB, user 1.6s, sys 8.2s, output queue size 11
progress 80% @chr18:21000001, elapsed 0.4s, est remaining 0.1s, peak mem 150MB, user 1.9s, sys 8.6s, output queue size 9
progress 85% @chr20:20000001, elapsed 0.4s, est remaining 0.1s, peak mem 151MB, user 2.0s, sys 9.0s, output queue size 66
progress 90% @chrX:17000001, elapsed 0.4s, est remaining 0.0s, peak mem 153MB, user 2.2s, sys 9.5s, output queue size 6
progress 95% @chrY:21000001, elapsed 0.4s, est remaining 0.0s, peak mem 154MB, user 2.5s, sys 9.9s, output queue size 5
progress 100% @HLA-A*02:01:01:04:1, elapsed 0.5s, est remaining 0.0s, peak mem 157MB, user 2.6s, sys 10.1s, output queue size 2344
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: 13775988
reads: 229053
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 0.633 user 4.948 sys 6.054 real
done: 1 calls 0.032 user 0.000 sys 0.038 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.001 real
execute: 1 calls 0.005 user 0.003 sys 0.460 real
idle: 74 calls 0.001 user 0.002 sys 31.127 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 165449728 mem 3.136 user 11.047 sys 1.970 real