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/7b/860f8d990b8b37145f3b60cf0394ff/.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/7b/860f8d990b8b37145f3b60cf0394ff/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4595d57f2512c3edbf9d75d6f729ae/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4595d57f2512c3edbf9d75d6f729ae/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% @chr1:161000001, elapsed 0.0s, est remaining 0.4s, peak mem 114MB, user 0.0s, sys 0.3s, output queue size 2
progress 10% @chr2:71000001, elapsed 0.0s, est remaining 0.4s, peak mem 114MB, user 0.1s, sys 0.9s, output queue size 2
progress 15% @chr2:233000001, elapsed 0.1s, est remaining 0.4s, peak mem 114MB, user 0.2s, sys 1.5s, output queue size 2
progress 20% @chr3:151000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.3s, sys 2.1s, output queue size 2
progress 25% @chr4:114000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.4s, sys 2.6s, output queue size 1
progress 30% @chr5:85000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.4s, sys 3.2s, output queue size 1
progress 35% @chr6:64000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.4s, sys 3.8s, output queue size 1
progress 40% @chr7:54000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.5s, sys 4.3s, output queue size 1
progress 45% @chr8:56000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.6s, sys 4.8s, output queue size 1
progress 50% @chr9:72000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.6s, sys 5.4s, output queue size 2
progress 55% @chr10:94000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.7s, sys 5.9s, output queue size 1
progress 60% @chr11:121000001, elapsed 0.3s, est remaining 0.2s, peak mem 114MB, user 0.7s, sys 6.6s, output queue size 2
progress 65% @chr13:17000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 0.9s, sys 7.2s, output queue size 1
progress 70% @chr14:62000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 1.0s, sys 7.7s, output queue size 1
progress 75% @chr16:13000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 1.1s, sys 8.3s, output queue size 2
progress 80% @chr17:82000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 1.1s, sys 8.8s, output queue size 2
progress 85% @chr20:20000001, elapsed 0.4s, est remaining 0.1s, peak mem 114MB, user 1.1s, sys 9.4s, output queue size 2
progress 90% @chrX:41000001, elapsed 0.4s, est remaining 0.0s, peak mem 138MB, user 1.4s, sys 9.7s, output queue size 114
progress 95% @chrY:36000001, elapsed 0.4s, est remaining 0.0s, peak mem 156MB, user 1.9s, sys 10.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 0.8s, est remaining 0.0s, peak mem 181MB, user 3.7s, sys 10.7s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50813906
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.511 user 5.630 sys 7.169 real
done: 1 calls 0.000 user 0.000 sys 0.008 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.002 sys 0.785 real
idle: 80 calls 0.019 user 0.037 sys 40.184 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 190623744 mem 4.207 user 11.382 sys 2.347 real