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/97/59f8cb861d24253906b61924dab175/.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/97/59f8cb861d24253906b61924dab175/.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
==> 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% @chr1:172000001, elapsed 0.0s, est remaining 0.9s, peak mem 103MB, user 0.1s, sys 0.9s, output queue size 17
progress 10% @chr2:72000001, elapsed 0.1s, est remaining 0.8s, peak mem 103MB, user 0.3s, sys 1.9s, output queue size 6
progress 15% @chr2:222000001, elapsed 0.1s, est remaining 0.7s, peak mem 103MB, user 0.5s, sys 2.9s, output queue size 13
progress 20% @chr3:163000001, elapsed 0.2s, est remaining 0.7s, peak mem 103MB, user 0.6s, sys 4.0s, output queue size 8
progress 25% @chr4:104000001, elapsed 0.2s, est remaining 0.6s, peak mem 103MB, user 0.8s, sys 5.0s, output queue size 11
progress 30% @chr5:71000001, elapsed 0.2s, est remaining 0.6s, peak mem 103MB, user 1.0s, sys 6.0s, output queue size 15
progress 35% @chr6:78000001, elapsed 0.3s, est remaining 0.5s, peak mem 103MB, user 1.1s, sys 7.0s, output queue size 10
progress 40% @chr7:74000001, elapsed 0.3s, est remaining 0.5s, peak mem 103MB, user 1.3s, sys 8.0s, output queue size 7
progress 45% @chr8:61000001, elapsed 0.4s, est remaining 0.4s, peak mem 103MB, user 1.4s, sys 9.1s, output queue size 7
progress 50% @chr9:87000001, elapsed 0.4s, est remaining 0.4s, peak mem 103MB, user 1.6s, sys 10.1s, output queue size 10
progress 55% @chr10:94000001, elapsed 0.4s, est remaining 0.4s, peak mem 103MB, user 1.7s, sys 11.2s, output queue size 8
progress 60% @chr11:118000001, elapsed 0.5s, est remaining 0.3s, peak mem 103MB, user 1.8s, sys 12.2s, output queue size 10
progress 65% @chr13:28000001, elapsed 0.5s, est remaining 0.3s, peak mem 103MB, user 2.0s, sys 13.3s, output queue size 8
progress 70% @chr14:65000001, elapsed 0.6s, est remaining 0.2s, peak mem 103MB, user 2.2s, sys 14.3s, output queue size 8
progress 75% @chr16:28000001, elapsed 0.6s, est remaining 0.2s, peak mem 103MB, user 2.3s, sys 15.4s, output queue size 10
progress 80% @chr17:74000001, elapsed 0.6s, est remaining 0.2s, peak mem 103MB, user 2.5s, sys 16.4s, output queue size 10
progress 85% @chr20:11000001, elapsed 0.7s, est remaining 0.1s, peak mem 103MB, user 2.6s, sys 17.4s, output queue size 11
progress 90% @chrX:34000001, elapsed 0.8s, est remaining 0.1s, peak mem 142MB, user 3.3s, sys 17.9s, output queue size 114
progress 95% @chrY:33000001, elapsed 0.8s, est remaining 0.0s, peak mem 159MB, user 3.9s, sys 18.7s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.2s, est remaining 0.0s, peak mem 187MB, user 6.0s, sys 19.8s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: bfebfbff 7ffefbff
  extended: d39ff7eb 00000818
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 31 max 96
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50813906
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 2.100 user 10.252 sys 12.821 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.008 user 0.001 sys 1.255 real
idle: 80 calls 0.014 user 0.031 sys 42.435 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 197021696 mem 6.430 user 20.907 sys 2.484 real