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/0b/585506cb076ab6ecc8a7724365a590/.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/54/67e80fd959906794093fa1156b5149/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/585506cb076ab6ecc8a7724365a590/.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
  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_BL.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_BL_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.
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% @chr1:160000001, elapsed 60.1s, est remaining 1141.1s, peak mem 112MB, user 0.1s, sys 0.7s, output queue size 1
progress 10% @chr2:79000001, elapsed 60.1s, est remaining 540.8s, peak mem 112MB, user 0.1s, sys 1.6s, output queue size 7
progress 15% @chr2:239000001, elapsed 60.1s, est remaining 340.7s, peak mem 112MB, user 0.3s, sys 2.4s, output queue size 17
progress 20% @chr3:132000001, elapsed 60.1s, est remaining 240.6s, peak mem 112MB, user 0.3s, sys 3.3s, output queue size 21
progress 25% @chr4:108000001, elapsed 60.2s, est remaining 180.5s, peak mem 112MB, user 0.4s, sys 4.1s, output queue size 23
progress 30% @chr5:89000001, elapsed 60.2s, est remaining 140.5s, peak mem 112MB, user 0.5s, sys 4.9s, output queue size 17
progress 35% @chr6:70000001, elapsed 60.2s, est remaining 111.9s, peak mem 112MB, user 0.6s, sys 5.7s, output queue size 21
progress 40% @chr7:57000001, elapsed 60.3s, est remaining 90.4s, peak mem 112MB, user 0.6s, sys 6.6s, output queue size 20
progress 45% @chr8:57000001, elapsed 60.3s, est remaining 73.7s, peak mem 112MB, user 0.7s, sys 7.4s, output queue size 11
progress 50% @chr9:75000001, elapsed 60.3s, est remaining 60.3s, peak mem 112MB, user 0.7s, sys 8.3s, output queue size 20
progress 55% @chr10:96000001, elapsed 60.4s, est remaining 49.4s, peak mem 112MB, user 0.8s, sys 9.1s, output queue size 9
progress 60% @chr11:122000001, elapsed 60.4s, est remaining 40.3s, peak mem 112MB, user 0.9s, sys 9.9s, output queue size 7
progress 65% @chr12:122000001, elapsed 60.4s, est remaining 32.5s, peak mem 112MB, user 1.0s, sys 10.8s, output queue size 27
progress 70% @chr14:60000001, elapsed 60.4s, est remaining 25.9s, peak mem 112MB, user 1.1s, sys 11.4s, output queue size 17
progress 75% @chr16:14000001, elapsed 60.5s, est remaining 20.2s, peak mem 112MB, user 1.2s, sys 12.2s, output queue size 24
progress 80% @chr18:1, elapsed 60.5s, est remaining 15.1s, peak mem 112MB, user 1.2s, sys 13.0s, output queue size 21
progress 85% @chr20:18000001, elapsed 60.5s, est remaining 10.7s, peak mem 112MB, user 1.3s, sys 13.8s, output queue size 4
progress 90% @chrX:39000001, elapsed 60.6s, est remaining 6.7s, peak mem 139MB, user 1.7s, sys 14.3s, output queue size 114
progress 95% @chrY:36000001, elapsed 60.6s, est remaining 3.2s, peak mem 157MB, user 2.1s, sys 15.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 60.9s, est remaining 0.0s, peak mem 175MB, user 3.4s, sys 16.1s, 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: 51395352
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.104 user 8.233 sys 9.881 real
done: 1 calls 0.011 user 0.000 sys 0.011 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.001 sys 60.935 real
idle: 61 calls 0.013 user 0.011 sys 38.778 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 184311808 mem 3.847 user 16.863 sys 62.408 real