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/8a/4b8b0e52b95350ea3d6ca0c968bed2/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.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/8a/4b8b0e52b95350ea3d6ca0c968bed2/.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/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/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.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_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 0.0s, est remaining 0.5s, peak mem 115MB, user 0.1s, sys 0.3s, output queue size 1
progress 10% @chr2:74000001, elapsed 0.0s, est remaining 0.4s, peak mem 115MB, user 0.2s, sys 0.8s, output queue size 6
progress 15% @chr2:235000001, elapsed 0.1s, est remaining 0.4s, peak mem 115MB, user 0.3s, sys 1.4s, output queue size 3
progress 20% @chr3:156000001, elapsed 0.1s, est remaining 0.3s, peak mem 115MB, user 0.4s, sys 1.9s, output queue size 4
progress 25% @chr4:116000001, elapsed 0.1s, est remaining 0.3s, peak mem 115MB, user 0.4s, sys 2.4s, output queue size 4
progress 30% @chr5:84000001, elapsed 0.1s, est remaining 0.3s, peak mem 115MB, user 0.5s, sys 3.0s, output queue size 4
progress 35% @chr6:63000001, elapsed 0.1s, est remaining 0.3s, peak mem 115MB, user 0.6s, sys 3.6s, output queue size 4
progress 40% @chr7:57000001, elapsed 0.2s, est remaining 0.2s, peak mem 115MB, user 0.6s, sys 4.2s, output queue size 18
progress 45% @chr8:56000001, elapsed 0.2s, est remaining 0.2s, peak mem 115MB, user 0.7s, sys 4.7s, output queue size 5
progress 50% @chr9:73000001, elapsed 0.2s, est remaining 0.2s, peak mem 115MB, user 0.8s, sys 5.2s, output queue size 7
progress 55% @chr10:95000001, elapsed 0.2s, est remaining 0.2s, peak mem 115MB, user 0.8s, sys 5.8s, output queue size 6
progress 60% @chr11:118000001, elapsed 0.2s, est remaining 0.2s, peak mem 115MB, user 0.9s, sys 6.3s, output queue size 5
progress 65% @chr13:17000001, elapsed 0.3s, est remaining 0.1s, peak mem 115MB, user 0.9s, sys 6.9s, output queue size 4
progress 70% @chr14:60000001, elapsed 0.3s, est remaining 0.1s, peak mem 115MB, user 1.0s, sys 7.5s, output queue size 1
progress 75% @chr16:13000001, elapsed 0.3s, est remaining 0.1s, peak mem 115MB, user 1.0s, sys 8.0s, output queue size 12
progress 80% @chr17:81000001, elapsed 0.3s, est remaining 0.1s, peak mem 115MB, user 1.2s, sys 8.5s, output queue size 4
progress 85% @chr20:22000001, elapsed 0.3s, est remaining 0.1s, peak mem 115MB, user 1.3s, sys 8.9s, output queue size 14
progress 90% @chrX:39000001, elapsed 0.4s, est remaining 0.0s, peak mem 145MB, user 1.7s, sys 9.2s, output queue size 114
progress 95% @chrY:37000001, elapsed 0.4s, est remaining 0.0s, peak mem 157MB, user 2.0s, sys 9.7s, output queue size 276
progress 100% @chr21:41000001, elapsed 0.9s, est remaining 0.0s, peak mem 182MB, user 3.7s, sys 10.1s, 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 1.180 user 5.265 sys 6.629 real
done: 1 calls 0.000 user 0.000 sys 0.007 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.003 sys 0.912 real
idle: 76 calls 0.010 user 0.020 sys 44.337 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 193101824 mem 4.178 user 11.002 sys 2.412 real