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/af/a67c91a799afbc04a3e751b8c81dff/.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-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_postQC_hg38.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/a67c91a799afbc04a3e751b8c81dff/.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/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_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 0.0s, est remaining 0.4s, peak mem 103MB, user 0.1s, sys 0.2s, output queue size 1
progress 10% @chr2:72000001, elapsed 0.0s, est remaining 0.3s, peak mem 103MB, user 0.1s, sys 0.6s, output queue size 4
progress 15% @chr2:232000001, elapsed 0.1s, est remaining 0.3s, peak mem 103MB, user 0.1s, sys 1.1s, output queue size 3
progress 20% @chr3:152000001, elapsed 0.1s, est remaining 0.3s, peak mem 103MB, user 0.2s, sys 1.7s, output queue size 1
progress 25% @chr4:117000001, elapsed 0.1s, est remaining 0.3s, peak mem 103MB, user 0.2s, sys 2.3s, output queue size 5
progress 30% @chr5:85000001, elapsed 0.1s, est remaining 0.3s, peak mem 103MB, user 0.3s, sys 2.8s, output queue size 1
progress 35% @chr6:65000001, elapsed 0.1s, est remaining 0.2s, peak mem 103MB, user 0.3s, sys 3.1s, output queue size 1
progress 40% @chr7:55000001, elapsed 0.1s, est remaining 0.2s, peak mem 103MB, user 0.3s, sys 3.7s, output queue size 1
progress 45% @chr8:52000001, elapsed 0.2s, est remaining 0.2s, peak mem 103MB, user 0.3s, sys 4.2s, output queue size 5
progress 50% @chr9:69000001, elapsed 0.2s, est remaining 0.2s, peak mem 103MB, user 0.4s, sys 4.8s, output queue size 4
progress 55% @chr10:91000001, elapsed 0.2s, est remaining 0.2s, peak mem 103MB, user 0.5s, sys 5.3s, output queue size 4
progress 60% @chr11:122000001, elapsed 0.2s, est remaining 0.1s, peak mem 103MB, user 0.5s, sys 5.7s, output queue size 3
progress 65% @chr13:17000001, elapsed 0.2s, est remaining 0.1s, peak mem 103MB, user 0.6s, sys 6.1s, output queue size 2
progress 70% @chr14:61000001, elapsed 0.3s, est remaining 0.1s, peak mem 103MB, user 0.6s, sys 6.6s, output queue size 1
progress 75% @chr16:12000001, elapsed 0.3s, est remaining 0.1s, peak mem 103MB, user 0.7s, sys 7.2s, output queue size 1
progress 80% @chr18:1, elapsed 0.3s, est remaining 0.1s, peak mem 103MB, user 0.7s, sys 7.7s, output queue size 4
progress 85% @chr20:22000001, elapsed 0.3s, est remaining 0.1s, peak mem 103MB, user 0.8s, sys 8.1s, output queue size 2
progress 90% @chrX:39000001, elapsed 0.3s, est remaining 0.0s, peak mem 145MB, user 1.0s, sys 8.5s, output queue size 114
progress 95% @chrY:38000001, elapsed 0.4s, est remaining 0.0s, peak mem 161MB, user 1.3s, sys 8.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 0.8s, est remaining 0.0s, peak mem 182MB, user 2.8s, sys 9.4s, output queue size 3664
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 96
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50813899
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.224 user 4.757 sys 6.202 real
done: 1 calls 0.000 user 0.000 sys 0.001 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.001 sys 0.808 real
idle: 76 calls 0.007 user 0.015 sys 42.910 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 191152128 mem 2.930 user 10.002 sys 1.975 real