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/fd/e35a7f1a1d2f25f4c9aadcc2d760f9/.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/fd/e35a7f1a1d2f25f4c9aadcc2d760f9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/6deb667df284430001177d0a9637ad/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/6deb667df284430001177d0a9637ad/HCC1395_tumor.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.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 HCC1395_tumor.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 HCC1395_tumor_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% @chr1:164000001, elapsed 0.0s, est remaining 0.9s, peak mem 108MB, user 0.1s, sys 1.0s, output queue size 16
progress 10% @chr2:80000001, elapsed 0.1s, est remaining 0.8s, peak mem 108MB, user 0.2s, sys 2.2s, output queue size 25
progress 15% @chr2:219000001, elapsed 0.1s, est remaining 0.8s, peak mem 108MB, user 0.3s, sys 3.7s, output queue size 16
progress 20% @chr3:175000001, elapsed 0.2s, est remaining 0.8s, peak mem 108MB, user 0.4s, sys 5.2s, output queue size 36
progress 25% @chr4:136000001, elapsed 0.3s, est remaining 0.8s, peak mem 108MB, user 0.4s, sys 7.8s, output queue size 19
progress 30% @chr5:79000001, elapsed 0.4s, est remaining 0.8s, peak mem 108MB, user 0.5s, sys 10.0s, output queue size 61
progress 35% @chr6:87000001, elapsed 0.4s, est remaining 0.8s, peak mem 108MB, user 0.6s, sys 12.3s, output queue size 21
progress 40% @chr7:79000001, elapsed 0.5s, est remaining 0.8s, peak mem 108MB, user 0.6s, sys 14.6s, output queue size 11
progress 45% @chr8:45000001, elapsed 0.6s, est remaining 0.7s, peak mem 108MB, user 0.7s, sys 17.0s, output queue size 14
progress 50% @chr9:61000001, elapsed 0.7s, est remaining 0.7s, peak mem 108MB, user 0.8s, sys 19.2s, output queue size 16
progress 55% @chr10:118000001, elapsed 0.7s, est remaining 0.6s, peak mem 108MB, user 0.9s, sys 21.4s, output queue size 16
progress 60% @chr11:117000001, elapsed 0.8s, est remaining 0.5s, peak mem 108MB, user 1.0s, sys 23.6s, output queue size 10
progress 65% @chr13:7000001, elapsed 0.9s, est remaining 0.5s, peak mem 108MB, user 1.1s, sys 25.7s, output queue size 18
progress 70% @chr14:55000001, elapsed 1.0s, est remaining 0.4s, peak mem 108MB, user 1.1s, sys 27.8s, output queue size 10
progress 75% @chr16:3000001, elapsed 1.0s, est remaining 0.3s, peak mem 108MB, user 1.2s, sys 30.0s, output queue size 10
progress 80% @chr18:12000001, elapsed 1.1s, est remaining 0.3s, peak mem 108MB, user 1.3s, sys 32.0s, output queue size 18
progress 85% @chr20:1000001, elapsed 1.2s, est remaining 0.2s, peak mem 108MB, user 1.4s, sys 34.1s, output queue size 21
progress 90% @chrX:48000001, elapsed 1.3s, est remaining 0.1s, peak mem 111MB, user 2.0s, sys 35.4s, output queue size 114
progress 95% @chrY:21000001, elapsed 1.3s, est remaining 0.1s, peak mem 126MB, user 2.5s, sys 37.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.7s, est remaining 0.0s, peak mem 156MB, user 3.8s, sys 39.9s, output queue size 3664
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 384
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50813895
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.207 user 20.349 sys 22.555 real
done: 1 calls 0.007 user 0.000 sys 0.010 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.002 sys 1.709 real
idle: 73 calls 0.008 user 0.015 sys 38.840 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 163663872 mem 4.158 user 40.709 sys 3.206 real