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/4f/8a8fddbedfd2279d6527b93a2341ff/.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/4f/8a8fddbedfd2279d6527b93a2341ff/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/694ac635125460463499fa86a79084/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/694ac635125460463499fa86a79084/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% @chr1:161000001, elapsed 0.0s, est remaining 0.5s, peak mem 114MB, user 0.1s, sys 0.4s, output queue size 8
progress 10% @chr2:50000001, elapsed 0.0s, est remaining 0.4s, peak mem 114MB, user 0.1s, sys 0.9s, output queue size 23
progress 15% @chr2:232000001, elapsed 0.1s, est remaining 0.4s, peak mem 114MB, user 0.3s, sys 1.4s, output queue size 6
progress 20% @chr3:153000001, elapsed 0.1s, est remaining 0.4s, peak mem 114MB, user 0.3s, sys 1.9s, output queue size 9
progress 25% @chr4:113000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.4s, sys 2.6s, output queue size 7
progress 30% @chr5:86000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.5s, sys 3.0s, output queue size 18
progress 35% @chr6:67000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.5s, sys 3.7s, output queue size 7
progress 40% @chr7:56000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.6s, sys 4.4s, output queue size 18
progress 45% @chr8:56000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.6s, sys 5.0s, output queue size 20
progress 50% @chr9:75000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.7s, sys 5.6s, output queue size 9
progress 55% @chr10:97000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.7s, sys 6.1s, output queue size 15
progress 60% @chr11:122000001, elapsed 0.3s, est remaining 0.2s, peak mem 114MB, user 0.7s, sys 6.8s, output queue size 7
progress 65% @chr13:14000001, elapsed 0.3s, est remaining 0.2s, peak mem 114MB, user 0.8s, sys 7.4s, output queue size 14
progress 70% @chr14:63000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 0.9s, sys 7.9s, output queue size 18
progress 75% @chr16:14000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 0.9s, sys 8.6s, output queue size 19
progress 80% @chr17:60000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 0.9s, sys 9.2s, output queue size 24
progress 85% @chr20:22000001, elapsed 0.4s, est remaining 0.1s, peak mem 114MB, user 1.0s, sys 9.8s, output queue size 19
progress 90% @chrX:38000001, elapsed 0.4s, est remaining 0.0s, peak mem 144MB, user 1.4s, sys 10.1s, output queue size 114
progress 95% @chrY:37000001, elapsed 0.4s, est remaining 0.0s, peak mem 159MB, user 1.6s, sys 10.7s, output queue size 276
progress 100% @chr21:41000001, elapsed 0.7s, est remaining 0.0s, peak mem 180MB, user 3.1s, sys 11.4s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 50813900
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.201 user 5.997 sys 7.295 real
done: 1 calls 0.005 user 0.000 sys 0.007 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.010 user 0.000 sys 0.735 real
idle: 75 calls 0.019 user 0.015 sys 38.356 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 189042688 mem 3.561 user 12.143 sys 2.212 real