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/3b/d72092da17a6fefc8bf267f5807e49/.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-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/FINAL_hotspot_list_07302025_hg38_sorted.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/67e80fd959906794093fa1156b5149/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/d72092da17a6fefc8bf267f5807e49/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/67e80fd959906794093fa1156b5149/HCC1395_BL.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_BL.md.bam --algo HsMetricAlgo --targets_list targets/FINAL_hotspot_list_07302025_hg38_sorted.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_BL_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
progress 5% @chr1:162000001, elapsed 120.1s, est remaining 2281.0s, peak mem 101MB, user 0.1s, sys 0.6s, output queue size 56
progress 10% @chr2:77000001, elapsed 120.1s, est remaining 1080.7s, peak mem 101MB, user 0.2s, sys 1.4s, output queue size 37
progress 15% @chr2:235000001, elapsed 120.1s, est remaining 680.6s, peak mem 101MB, user 0.2s, sys 2.2s, output queue size 30
progress 20% @chr3:155000001, elapsed 120.1s, est remaining 480.5s, peak mem 101MB, user 0.3s, sys 2.9s, output queue size 65
progress 25% @chr4:116000001, elapsed 120.2s, est remaining 360.5s, peak mem 101MB, user 0.4s, sys 3.7s, output queue size 34
progress 30% @chr5:89000001, elapsed 120.2s, est remaining 280.4s, peak mem 101MB, user 0.4s, sys 4.6s, output queue size 54
progress 35% @chr6:67000001, elapsed 120.2s, est remaining 223.3s, peak mem 101MB, user 0.5s, sys 5.4s, output queue size 67
progress 40% @chr7:58000001, elapsed 120.2s, est remaining 180.4s, peak mem 101MB, user 0.5s, sys 6.1s, output queue size 41
progress 45% @chr8:57000001, elapsed 120.3s, est remaining 147.0s, peak mem 101MB, user 0.6s, sys 6.9s, output queue size 4
progress 50% @chr9:73000001, elapsed 120.3s, est remaining 120.3s, peak mem 101MB, user 0.7s, sys 7.9s, output queue size 72
progress 55% @chr10:96000001, elapsed 120.3s, est remaining 98.5s, peak mem 101MB, user 0.8s, sys 8.8s, output queue size 28
progress 60% @chr11:123000001, elapsed 120.4s, est remaining 80.2s, peak mem 101MB, user 0.8s, sys 9.7s, output queue size 3
progress 65% @chr13:16000001, elapsed 120.4s, est remaining 64.8s, peak mem 101MB, user 0.9s, sys 10.6s, output queue size 63
progress 70% @chr14:62000001, elapsed 120.4s, est remaining 51.6s, peak mem 101MB, user 0.9s, sys 11.5s, output queue size 34
progress 75% @chr16:12000001, elapsed 120.5s, est remaining 40.2s, peak mem 101MB, user 1.0s, sys 12.5s, output queue size 3
progress 80% @chr18:2000001, elapsed 120.5s, est remaining 30.1s, peak mem 101MB, user 1.0s, sys 13.5s, output queue size 66
progress 85% @chr20:22000001, elapsed 120.5s, est remaining 21.3s, peak mem 101MB, user 1.0s, sys 14.4s, output queue size 37
progress 90% @chrX:37000001, elapsed 120.6s, est remaining 13.4s, peak mem 144MB, user 1.5s, sys 14.9s, output queue size 114
progress 95% @chrY:37000001, elapsed 120.6s, est remaining 6.3s, peak mem 163MB, user 1.9s, sys 15.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 120.9s, est remaining 0.0s, peak mem 178MB, user 3.0s, sys 16.3s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 51395352
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.483 user 8.535 sys 9.902 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 0.004 user 0.001 sys 120.930 real
idle: 61 calls 0.005 user 0.018 sys 39.022 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 186961920 mem 3.177 user 16.903 sys 122.090 real