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/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/c34f97e22c19530eccfbd202db6143/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/c34f97e22c19530eccfbd202db6143/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/35a94f5f725d1d5241d0808d9af182/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/35a94f5f725d1d5241d0808d9af182/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% @chr1:159000001, elapsed 0.0s, est remaining 0.6s, peak mem 102MB, user 0.0s, sys 0.5s, output queue size 17
progress 10% @chr2:72000001, elapsed 0.1s, est remaining 0.5s, peak mem 102MB, user 0.1s, sys 1.3s, output queue size 5
progress 15% @chr2:234000001, elapsed 0.1s, est remaining 0.5s, peak mem 102MB, user 0.2s, sys 2.2s, output queue size 6
progress 20% @chr3:155000001, elapsed 0.1s, est remaining 0.5s, peak mem 102MB, user 0.2s, sys 2.9s, output queue size 9
progress 25% @chr4:115000001, elapsed 0.1s, est remaining 0.4s, peak mem 102MB, user 0.3s, sys 3.6s, output queue size 3
progress 30% @chr5:84000001, elapsed 0.2s, est remaining 0.4s, peak mem 102MB, user 0.3s, sys 4.5s, output queue size 2
progress 35% @chr6:68000001, elapsed 0.2s, est remaining 0.4s, peak mem 102MB, user 0.4s, sys 5.3s, output queue size 12
progress 40% @chr7:55000001, elapsed 0.2s, est remaining 0.3s, peak mem 102MB, user 0.4s, sys 6.1s, output queue size 3
progress 45% @chr8:56000001, elapsed 0.3s, est remaining 0.3s, peak mem 102MB, user 0.5s, sys 6.8s, output queue size 1
progress 50% @chr9:74000001, elapsed 0.3s, est remaining 0.3s, peak mem 102MB, user 0.5s, sys 7.7s, output queue size 7
progress 55% @chr10:95000001, elapsed 0.3s, est remaining 0.3s, peak mem 102MB, user 0.5s, sys 8.5s, output queue size 7
progress 60% @chr11:123000001, elapsed 0.3s, est remaining 0.2s, peak mem 102MB, user 0.6s, sys 9.3s, output queue size 5
progress 65% @chr13:12000001, elapsed 0.4s, est remaining 0.2s, peak mem 102MB, user 0.6s, sys 10.0s, output queue size 12
progress 70% @chr14:62000001, elapsed 0.4s, est remaining 0.2s, peak mem 102MB, user 0.7s, sys 10.9s, output queue size 8
progress 75% @chr16:15000001, elapsed 0.4s, est remaining 0.1s, peak mem 102MB, user 0.7s, sys 11.7s, output queue size 8
progress 80% @chr18:1, elapsed 0.4s, est remaining 0.1s, peak mem 102MB, user 0.8s, sys 12.3s, output queue size 2
progress 85% @chr20:22000001, elapsed 0.5s, est remaining 0.1s, peak mem 102MB, user 0.8s, sys 13.2s, output queue size 12
progress 90% @chrX:34000001, elapsed 0.5s, est remaining 0.1s, peak mem 129MB, user 1.3s, sys 13.8s, output queue size 114
progress 95% @chrY:32000001, elapsed 0.6s, est remaining 0.0s, peak mem 141MB, user 1.6s, sys 14.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.0s, est remaining 0.0s, peak mem 160MB, user 2.8s, sys 15.8s, 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: 52292891
reads: 1001133
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.107 user 8.050 sys 9.562 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 0.006 user 0.002 sys 1.037 real
idle: 74 calls 0.009 user 0.028 sys 43.621 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 168583168 mem 2.920 user 16.464 sys 2.193 real