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/2c/550f3a87a3ad97e41b3e1476b3345a/.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/10/9c315bb6e7871cb298609d78a3f103/1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/550f3a87a3ad97e41b3e1476b3345a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/9c315bb6e7871cb298609d78a3f103/1136_76X-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
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed
==> STAGING COMPLETE (8 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam --algo HsMetricAlgo --targets_list targets/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_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 1136_76X-T1-TDNA-1_A23MHWWLT4_1_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:181000001, elapsed 4.6s, est remaining 87.0s, peak mem 3103MB, user 104.4s, sys 2.4s, output queue size 146
progress 10% @chr2:90000001, elapsed 7.8s, est remaining 70.3s, peak mem 4128MB, user 214.9s, sys 4.2s, output queue size 166
progress 15% @chr2:74000001, elapsed 11.1s, est remaining 63.0s, peak mem 5253MB, user 319.0s, sys 6.0s, output queue size 161
progress 20% @chr3:167000001, elapsed 14.3s, est remaining 57.2s, peak mem 5268MB, user 416.2s, sys 6.9s, output queue size 141
progress 25% @chr4:124000001, elapsed 16.9s, est remaining 50.7s, peak mem 5443MB, user 494.9s, sys 7.5s, output queue size 302
progress 30% @chr5:104000001, elapsed 18.9s, est remaining 44.0s, peak mem 5475MB, user 554.1s, sys 8.1s, output queue size 464
progress 35% @chr6:79000001, elapsed 22.2s, est remaining 41.2s, peak mem 5907MB, user 643.0s, sys 8.8s, output queue size 429
progress 40% @chr7:45000001, elapsed 25.5s, est remaining 38.2s, peak mem 6073MB, user 745.1s, sys 9.7s, output queue size 197
progress 45% @chr8:70000001, elapsed 29.2s, est remaining 35.7s, peak mem 6410MB, user 851.9s, sys 10.7s, output queue size 356
progress 50% @chr9:77000001, elapsed 31.9s, est remaining 31.9s, peak mem 6504MB, user 940.6s, sys 11.4s, output queue size 324
progress 55% @chr10:86000001, elapsed 35.6s, est remaining 29.2s, peak mem 6660MB, user 1050.9s, sys 12.3s, output queue size 348
progress 60% @chr11:130000001, elapsed 39.8s, est remaining 26.5s, peak mem 6693MB, user 1188.6s, sys 13.1s, output queue size 136
progress 65% @chr13:26000001, elapsed 43.1s, est remaining 23.2s, peak mem 6777MB, user 1290.1s, sys 13.8s, output queue size 143
progress 70% @chr14:21000001, elapsed 45.3s, est remaining 19.4s, peak mem 6816MB, user 1361.5s, sys 14.4s, output queue size 299
progress 75% @chr16:41000001, elapsed 49.3s, est remaining 16.4s, peak mem 6816MB, user 1471.5s, sys 15.2s, output queue size 461
progress 80% @chr18:10000001, elapsed 55.9s, est remaining 14.0s, peak mem 6929MB, user 1646.6s, sys 16.3s, output queue size 623
progress 85% @chr19:57000001, elapsed 61.8s, est remaining 10.9s, peak mem 6929MB, user 1848.3s, sys 17.6s, output queue size 351
progress 90% @chr22:36000001, elapsed 65.2s, est remaining 7.2s, peak mem 6929MB, user 1975.5s, sys 18.4s, output queue size 78
progress 95% @chrY:54000001, elapsed 67.2s, est remaining 3.5s, peak mem 7020MB, user 2034.9s, sys 18.9s, output queue size 240
progress 100% @chr22:23000001, elapsed 74.4s, est remaining 0.0s, peak mem 7089MB, user 2100.4s, sys 19.6s, output queue size 3635
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: 57443072063
reads: 1090378638
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 926.403 user 17.098 sys 940.263 real
done: 1 calls 0.324 user 0.029 sys 0.362 real
exec_no_coor: 1 calls 0.008 user 0.000 sys 0.019 real
execute: 1 calls 0.002 user 0.001 sys 74.464 real
idle: 254 calls 0.151 user 0.001 sys 228.183 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 7433981952 mem 2102.234 user 20.243 sys 76.513 real