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/a7/ecdf965eec78afb19c3be338f2434d/.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/a7/ecdf965eec78afb19c3be338f2434d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/25dc077a00a8ba972f2936f02d2b56/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/25dc077a00a8ba972f2936f02d2b56/Sig_18_Blood.md.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_noncoding_postQC_hg38.bed
  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 Sig_18_Blood.md.bam --algo HsMetricAlgo --targets_list targets/altera_v3_targets_noncoding_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 Sig_18_Blood_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:156000001, elapsed 0.0s, est remaining 0.7s, peak mem 99MB, user 0.1s, sys 0.7s, output queue size 18
progress 10% @chr2:99000001, elapsed 0.1s, est remaining 0.8s, peak mem 99MB, user 0.1s, sys 2.1s, output queue size 10
progress 15% @chr2:233000001, elapsed 0.1s, est remaining 0.7s, peak mem 99MB, user 0.2s, sys 3.4s, output queue size 29
progress 20% @chr3:152000001, elapsed 0.2s, est remaining 0.7s, peak mem 99MB, user 0.3s, sys 4.7s, output queue size 19
progress 25% @chr4:114000001, elapsed 0.2s, est remaining 0.7s, peak mem 99MB, user 0.4s, sys 6.0s, output queue size 8
progress 30% @chr5:84000001, elapsed 0.3s, est remaining 0.6s, peak mem 99MB, user 0.5s, sys 7.2s, output queue size 23
progress 35% @chr6:36000001, elapsed 0.3s, est remaining 0.6s, peak mem 99MB, user 0.6s, sys 8.6s, output queue size 29
progress 40% @chr7:79000001, elapsed 0.4s, est remaining 0.5s, peak mem 99MB, user 0.6s, sys 9.9s, output queue size 24
progress 45% @chr8:81000001, elapsed 0.4s, est remaining 0.5s, peak mem 99MB, user 0.7s, sys 11.3s, output queue size 15
progress 50% @chr9:67000001, elapsed 0.4s, est remaining 0.4s, peak mem 99MB, user 0.8s, sys 12.6s, output queue size 23
progress 55% @chr10:118000001, elapsed 0.5s, est remaining 0.4s, peak mem 99MB, user 0.9s, sys 13.9s, output queue size 21
progress 60% @chr11:119000001, elapsed 0.5s, est remaining 0.4s, peak mem 99MB, user 1.0s, sys 15.2s, output queue size 21
progress 65% @chr13:10000001, elapsed 0.6s, est remaining 0.3s, peak mem 99MB, user 1.1s, sys 16.4s, output queue size 17
progress 70% @chr14:57000001, elapsed 0.6s, est remaining 0.3s, peak mem 99MB, user 1.2s, sys 17.8s, output queue size 14
progress 75% @chr16:5000001, elapsed 0.7s, est remaining 0.2s, peak mem 99MB, user 1.3s, sys 19.0s, output queue size 9
progress 80% @chr17:79000001, elapsed 0.7s, est remaining 0.2s, peak mem 99MB, user 1.4s, sys 20.4s, output queue size 7
progress 85% @chr20:19000001, elapsed 0.8s, est remaining 0.1s, peak mem 99MB, user 1.5s, sys 21.7s, output queue size 13
progress 90% @chrX:33000001, elapsed 0.8s, est remaining 0.1s, peak mem 108MB, user 2.0s, sys 22.8s, output queue size 114
progress 95% @chrY:26000001, elapsed 0.9s, est remaining 0.0s, peak mem 120MB, user 2.5s, sys 24.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.5s, est remaining 0.0s, peak mem 150MB, user 3.9s, sys 26.3s, 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 384
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 52290606
reads: 1001133
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.126 user 13.961 sys 15.003 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.004 user 0.001 sys 1.489 real
idle: 79 calls 0.007 user 0.026 sys 45.790 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 157442048 mem 4.169 user 26.872 sys 2.641 real