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/09/fbbe82abc2522d1ba5357854b30a4b/.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/09/fbbe82abc2522d1ba5357854b30a4b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/affe90ad272751a557cfb55ea8a87a/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/affe90ad272751a557cfb55ea8a87a/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 0.9s, peak mem 99MB, user 0.1s, sys 1.0s, output queue size 22
progress 10% @chr2:71000001, elapsed 0.1s, est remaining 0.8s, peak mem 99MB, user 0.1s, sys 2.2s, output queue size 25
progress 15% @chr2:237000001, elapsed 0.1s, est remaining 0.7s, peak mem 99MB, user 0.2s, sys 3.4s, output queue size 23
progress 20% @chr3:157000001, elapsed 0.2s, est remaining 0.7s, peak mem 99MB, user 0.3s, sys 4.7s, output queue size 14
progress 25% @chr4:114000001, elapsed 0.2s, est remaining 0.6s, peak mem 99MB, user 0.3s, sys 6.0s, output queue size 2
progress 30% @chr5:81000001, elapsed 0.3s, est remaining 0.6s, peak mem 99MB, user 0.4s, sys 7.5s, output queue size 35
progress 35% @chr6:61000001, elapsed 0.3s, est remaining 0.6s, peak mem 99MB, user 0.6s, sys 9.2s, output queue size 6
progress 40% @chr7:52000001, elapsed 0.4s, est remaining 0.6s, peak mem 99MB, user 0.7s, sys 10.8s, output queue size 14
progress 45% @chr8:41000001, elapsed 0.5s, est remaining 0.6s, peak mem 99MB, user 0.8s, sys 12.5s, output queue size 19
progress 50% @chr9:46000001, elapsed 0.5s, est remaining 0.5s, peak mem 99MB, user 0.8s, sys 14.4s, output queue size 27
progress 55% @chr10:77000001, elapsed 0.6s, est remaining 0.5s, peak mem 99MB, user 1.0s, sys 16.4s, output queue size 18
progress 60% @chr12:15000001, elapsed 0.6s, est remaining 0.4s, peak mem 99MB, user 1.1s, sys 18.1s, output queue size 23
progress 65% @chr12:130000001, elapsed 0.7s, est remaining 0.4s, peak mem 99MB, user 1.1s, sys 20.0s, output queue size 19
progress 70% @chr14:45000001, elapsed 0.8s, est remaining 0.3s, peak mem 99MB, user 1.2s, sys 21.8s, output queue size 23
progress 75% @chr16:36000001, elapsed 0.8s, est remaining 0.3s, peak mem 99MB, user 1.3s, sys 23.7s, output queue size 24
progress 80% @chr17:67000001, elapsed 0.9s, est remaining 0.2s, peak mem 99MB, user 1.4s, sys 25.6s, output queue size 20
progress 85% @chr20:1, elapsed 1.0s, est remaining 0.2s, peak mem 99MB, user 1.4s, sys 27.6s, output queue size 26
progress 90% @chr21:42000001, elapsed 1.0s, est remaining 0.1s, peak mem 108MB, user 1.8s, sys 29.1s, output queue size 114
progress 95% @chrY:26000001, elapsed 1.1s, est remaining 0.1s, peak mem 123MB, user 2.2s, sys 31.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.6s, est remaining 0.0s, peak mem 147MB, user 3.3s, sys 34.9s, 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: 50813903
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.117 user 18.219 sys 19.643 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 0.000 user 0.010 sys 1.636 real
idle: 75 calls 0.006 user 0.019 sys 42.387 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 154247168 mem 3.561 user 35.412 sys 2.796 real