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/34/68a85b2e63687a7d6a36eaf73fd9bb/.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/34/68a85b2e63687a7d6a36eaf73fd9bb/.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
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.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_minus_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_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:164000001, elapsed 0.0s, est remaining 0.7s, peak mem 114MB, user 0.1s, sys 0.6s, output queue size 4
progress 10% @chr2:72000001, elapsed 0.1s, est remaining 0.6s, peak mem 114MB, user 0.2s, sys 1.5s, output queue size 1
progress 15% @chr2:235000001, elapsed 0.1s, est remaining 0.6s, peak mem 114MB, user 0.3s, sys 2.4s, output queue size 8
progress 20% @chr3:152000001, elapsed 0.1s, est remaining 0.5s, peak mem 114MB, user 0.3s, sys 3.3s, output queue size 1
progress 25% @chr4:113000001, elapsed 0.2s, est remaining 0.5s, peak mem 114MB, user 0.4s, sys 4.2s, output queue size 2
progress 30% @chr5:86000001, elapsed 0.2s, est remaining 0.4s, peak mem 114MB, user 0.4s, sys 5.0s, output queue size 18
progress 35% @chr6:64000001, elapsed 0.2s, est remaining 0.4s, peak mem 114MB, user 0.5s, sys 5.9s, output queue size 1
progress 40% @chr7:55000001, elapsed 0.3s, est remaining 0.4s, peak mem 114MB, user 0.6s, sys 6.8s, output queue size 9
progress 45% @chr8:56000001, elapsed 0.3s, est remaining 0.4s, peak mem 114MB, user 0.6s, sys 7.8s, output queue size 1
progress 50% @chr9:71000001, elapsed 0.3s, est remaining 0.3s, peak mem 114MB, user 0.7s, sys 8.7s, output queue size 3
progress 55% @chr10:96000001, elapsed 0.4s, est remaining 0.3s, peak mem 114MB, user 0.7s, sys 9.6s, output queue size 15
progress 60% @chr11:119000001, elapsed 0.4s, est remaining 0.3s, peak mem 114MB, user 0.7s, sys 10.5s, output queue size 4
progress 65% @chr13:13000001, elapsed 0.4s, est remaining 0.2s, peak mem 114MB, user 0.8s, sys 11.5s, output queue size 2
progress 70% @chr14:61000001, elapsed 0.4s, est remaining 0.2s, peak mem 114MB, user 0.8s, sys 12.5s, output queue size 2
progress 75% @chr16:11000001, elapsed 0.5s, est remaining 0.2s, peak mem 114MB, user 0.9s, sys 13.4s, output queue size 2
progress 80% @chr18:1, elapsed 0.5s, est remaining 0.1s, peak mem 114MB, user 0.9s, sys 14.3s, output queue size 22
progress 85% @chr20:23000001, elapsed 0.5s, est remaining 0.1s, peak mem 114MB, user 1.0s, sys 15.2s, output queue size 9
progress 90% @chrX:39000001, elapsed 0.6s, est remaining 0.1s, peak mem 151MB, user 1.4s, sys 15.7s, output queue size 114
progress 95% @chrY:38000001, elapsed 0.6s, est remaining 0.0s, peak mem 166MB, user 1.7s, sys 16.3s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.0s, est remaining 0.0s, peak mem 193MB, user 3.4s, sys 17.1s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 31 max 128
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50811681
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.568 user 8.570 sys 10.348 real
done: 1 calls 0.004 user 0.000 sys 0.008 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.002 sys 0.969 real
idle: 81 calls 0.009 user 0.025 sys 39.746 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 204447744 mem 3.903 user 17.740 sys 2.519 real