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/f0/e7531e9527984100605a3397ae47aa/.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-rnd-pltf-dev-nextflow-scratch-01/work/f0/e7531e9527984100605a3397ae47aa/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/50dd12f94eeb22331190484c74ad72/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/50dd12f94eeb22331190484c74ad72/HCC1395_tumor.md.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_noncoding_postQC_hg38.bed
  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_noncoding_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_noncoding_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:156000001, elapsed 0.0s, est remaining 0.7s, peak mem 100MB, user 0.5s, sys 0.3s, output queue size 5
progress 10% @chr2:78000001, elapsed 0.1s, est remaining 0.6s, peak mem 100MB, user 0.9s, sys 0.7s, output queue size 16
progress 15% @chr2:198000001, elapsed 0.1s, est remaining 0.6s, peak mem 100MB, user 1.4s, sys 1.2s, output queue size 37
progress 20% @chr3:152000001, elapsed 0.1s, est remaining 0.5s, peak mem 100MB, user 1.8s, sys 1.8s, output queue size 4
progress 25% @chr4:122000001, elapsed 0.2s, est remaining 0.5s, peak mem 100MB, user 2.5s, sys 2.0s, output queue size 10
progress 30% @chr5:84000001, elapsed 0.2s, est remaining 0.5s, peak mem 100MB, user 3.1s, sys 2.5s, output queue size 29
progress 35% @chr6:68000001, elapsed 0.2s, est remaining 0.4s, peak mem 100MB, user 3.7s, sys 2.9s, output queue size 6
progress 40% @chr7:60000001, elapsed 0.3s, est remaining 0.4s, peak mem 100MB, user 4.5s, sys 3.0s, output queue size 6
progress 45% @chr8:63000001, elapsed 0.3s, est remaining 0.4s, peak mem 100MB, user 4.6s, sys 3.8s, output queue size 3
progress 50% @chr9:70000001, elapsed 0.3s, est remaining 0.3s, peak mem 100MB, user 5.3s, sys 4.2s, output queue size 3
progress 55% @chr10:102000001, elapsed 0.4s, est remaining 0.3s, peak mem 100MB, user 5.9s, sys 4.5s, output queue size 9
progress 60% @chr11:117000001, elapsed 0.4s, est remaining 0.3s, peak mem 100MB, user 6.4s, sys 5.0s, output queue size 7
progress 65% @chr13:17000001, elapsed 0.4s, est remaining 0.2s, peak mem 100MB, user 7.2s, sys 5.1s, output queue size 5
progress 70% @chr14:52000001, elapsed 0.4s, est remaining 0.2s, peak mem 100MB, user 7.8s, sys 5.5s, output queue size 21
progress 75% @chr16:9000001, elapsed 0.5s, est remaining 0.2s, peak mem 100MB, user 8.5s, sys 5.6s, output queue size 4
progress 80% @chr17:74000001, elapsed 0.5s, est remaining 0.1s, peak mem 100MB, user 9.3s, sys 5.7s, output queue size 10
progress 85% @chr20:19000001, elapsed 0.5s, est remaining 0.1s, peak mem 100MB, user 10.1s, sys 6.0s, output queue size 4
progress 90% @chrX:36000001, elapsed 0.6s, est remaining 0.1s, peak mem 133MB, user 10.7s, sys 6.5s, output queue size 114
progress 95% @chrY:34000001, elapsed 0.6s, est remaining 0.0s, peak mem 150MB, user 11.0s, sys 7.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.0s, est remaining 0.0s, peak mem 168MB, user 12.3s, sys 8.1s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50811681
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.175 user 4.410 sys 5.772 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 0.001 user 0.000 sys 1.023 real
idle: 76 calls 0.013 user 0.007 sys 41.259 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 176463872 mem 12.769 user 8.492 sys 2.178 real