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/d1/0cb608bbb17d0cd0402aa9cb628b82/.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/d1/0cb608bbb17d0cd0402aa9cb628b82/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/8330f830ccd1737ed07a692606e514/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/8330f830ccd1737ed07a692606e514/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
==> 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_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 HCC1395_tumor_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% @chr1:157000001, elapsed 0.1s, est remaining 1.2s, peak mem 108MB, user 0.1s, sys 1.4s, output queue size 18
progress 10% @chr2:31000001, elapsed 0.1s, est remaining 1.1s, peak mem 108MB, user 0.2s, sys 3.1s, output queue size 42
progress 15% @chr2:232000001, elapsed 0.2s, est remaining 1.0s, peak mem 108MB, user 0.2s, sys 4.7s, output queue size 38
progress 20% @chr3:149000001, elapsed 0.2s, est remaining 0.9s, peak mem 108MB, user 0.4s, sys 6.5s, output queue size 27
progress 25% @chr4:142000001, elapsed 0.3s, est remaining 0.9s, peak mem 108MB, user 0.5s, sys 8.3s, output queue size 42
progress 30% @chr5:81000001, elapsed 0.4s, est remaining 0.9s, peak mem 108MB, user 0.6s, sys 10.5s, output queue size 29
progress 35% @chr6:90000001, elapsed 0.4s, est remaining 0.8s, peak mem 108MB, user 0.6s, sys 12.6s, output queue size 52
progress 40% @chr7:49000001, elapsed 0.5s, est remaining 0.8s, peak mem 108MB, user 0.8s, sys 14.7s, output queue size 49
progress 45% @chr8:53000001, elapsed 0.6s, est remaining 0.7s, peak mem 108MB, user 0.9s, sys 16.9s, output queue size 55
progress 50% @chr9:100000001, elapsed 0.7s, est remaining 0.7s, peak mem 108MB, user 1.0s, sys 19.0s, output queue size 49
progress 55% @chr10:119000001, elapsed 0.7s, est remaining 0.6s, peak mem 108MB, user 1.1s, sys 21.1s, output queue size 54
progress 60% @chr11:116000001, elapsed 0.8s, est remaining 0.5s, peak mem 108MB, user 1.3s, sys 23.2s, output queue size 45
progress 65% @chr13:40000001, elapsed 0.9s, est remaining 0.5s, peak mem 108MB, user 1.4s, sys 25.4s, output queue size 52
progress 70% @chr14:53000001, elapsed 1.0s, est remaining 0.4s, peak mem 108MB, user 1.5s, sys 27.4s, output queue size 51
progress 75% @chr16:4000001, elapsed 1.0s, est remaining 0.3s, peak mem 108MB, user 1.5s, sys 29.6s, output queue size 34
progress 80% @chr18:24000001, elapsed 1.1s, est remaining 0.3s, peak mem 108MB, user 1.6s, sys 31.7s, output queue size 30
progress 85% @chr20:13000001, elapsed 1.2s, est remaining 0.2s, peak mem 108MB, user 1.7s, sys 33.8s, output queue size 59
progress 90% @chrX:47000001, elapsed 1.3s, est remaining 0.1s, peak mem 120MB, user 2.3s, sys 35.0s, output queue size 114
progress 95% @chrY:47000001, elapsed 1.3s, est remaining 0.1s, peak mem 132MB, user 2.7s, sys 36.7s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.9s, est remaining 0.0s, peak mem 159MB, user 4.3s, sys 39.5s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50813899
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.103 user 20.204 sys 21.747 real
done: 1 calls 0.007 user 0.000 sys 0.011 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.001 user 0.000 sys 1.889 real
idle: 83 calls 0.005 user 0.022 sys 44.439 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 166879232 mem 4.847 user 40.113 sys 3.422 real