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/a3/3c9703e2806260b16ccbe580b6ebf3/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_coding_postQC_hg38.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/a3/3c9703e2806260b16ccbe580b6ebf3/.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_coding_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_coding_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:152000001, elapsed 0.0s, est remaining 0.8s, peak mem 102MB, user 0.8s, sys 0.1s, output queue size 20
progress 10% @chr2:96000001, elapsed 0.1s, est remaining 0.7s, peak mem 102MB, user 1.4s, sys 0.7s, output queue size 21
progress 15% @chr2:230000001, elapsed 0.1s, est remaining 0.7s, peak mem 102MB, user 2.0s, sys 1.4s, output queue size 8
progress 20% @chr3:148000001, elapsed 0.2s, est remaining 0.7s, peak mem 102MB, user 2.8s, sys 1.9s, output queue size 16
progress 25% @chr4:107000001, elapsed 0.2s, est remaining 0.6s, peak mem 102MB, user 3.4s, sys 2.4s, output queue size 8
progress 30% @chr5:83000001, elapsed 0.2s, est remaining 0.6s, peak mem 102MB, user 4.5s, sys 2.6s, output queue size 23
progress 35% @chr6:66000001, elapsed 0.3s, est remaining 0.5s, peak mem 102MB, user 5.0s, sys 3.2s, output queue size 9
progress 40% @chr7:77000001, elapsed 0.3s, est remaining 0.5s, peak mem 102MB, user 6.0s, sys 3.6s, output queue size 8
progress 45% @chr8:52000001, elapsed 0.4s, est remaining 0.4s, peak mem 102MB, user 6.4s, sys 4.3s, output queue size 21
progress 50% @chr9:62000001, elapsed 0.4s, est remaining 0.4s, peak mem 102MB, user 7.0s, sys 4.9s, output queue size 13
progress 55% @chr10:87000001, elapsed 0.4s, est remaining 0.4s, peak mem 102MB, user 7.6s, sys 5.5s, output queue size 16
progress 60% @chr11:101000001, elapsed 0.5s, est remaining 0.3s, peak mem 102MB, user 8.0s, sys 6.3s, output queue size 23
progress 65% @chr13:10000001, elapsed 0.5s, est remaining 0.3s, peak mem 102MB, user 8.4s, sys 7.2s, output queue size 12
progress 70% @chr14:60000001, elapsed 0.6s, est remaining 0.2s, peak mem 102MB, user 9.0s, sys 7.7s, output queue size 7
progress 75% @chr16:6000001, elapsed 0.6s, est remaining 0.2s, peak mem 102MB, user 9.6s, sys 8.3s, output queue size 7
progress 80% @chr17:78000001, elapsed 0.6s, est remaining 0.2s, peak mem 102MB, user 10.5s, sys 8.6s, output queue size 6
progress 85% @chr19:45000001, elapsed 0.7s, est remaining 0.1s, peak mem 102MB, user 11.2s, sys 9.0s, output queue size 36
progress 90% @chrX:27000001, elapsed 0.7s, est remaining 0.1s, peak mem 114MB, user 12.0s, sys 9.6s, output queue size 114
progress 95% @chrY:29000001, elapsed 0.8s, est remaining 0.0s, peak mem 129MB, user 12.4s, sys 10.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.1s, est remaining 0.0s, peak mem 153MB, user 13.5s, sys 12.0s, 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 1.251 user 6.247 sys 7.500 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.001 sys 1.096 real
idle: 80 calls 0.019 user 0.014 sys 38.323 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 160534528 mem 13.928 user 12.386 sys 2.247 real