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/91/2ea014ae5f596c2f9661078d557193/.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/b8/f45ecce184d7704636c7db0c935580/HCC1395_BL.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/2ea014ae5f596c2f9661078d557193/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/f45ecce184d7704636c7db0c935580/HCC1395_BL.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 HCC1395_BL.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 HCC1395_BL_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:153000001, elapsed 0.0s, est remaining 0.8s, peak mem 101MB, user 0.1s, sys 0.8s, output queue size 8
progress 10% @chr2:67000001, elapsed 0.1s, est remaining 0.7s, peak mem 101MB, user 0.1s, sys 1.8s, output queue size 8
progress 15% @chr2:229000001, elapsed 0.1s, est remaining 0.6s, peak mem 101MB, user 0.2s, sys 2.7s, output queue size 9
progress 20% @chr3:173000001, elapsed 0.1s, est remaining 0.6s, peak mem 101MB, user 0.3s, sys 3.8s, output queue size 8
progress 25% @chr4:104000001, elapsed 0.2s, est remaining 0.5s, peak mem 101MB, user 0.4s, sys 4.7s, output queue size 11
progress 30% @chr5:79000001, elapsed 0.2s, est remaining 0.5s, peak mem 101MB, user 0.4s, sys 5.7s, output queue size 8
progress 35% @chr6:55000001, elapsed 0.3s, est remaining 0.5s, peak mem 101MB, user 0.5s, sys 6.7s, output queue size 10
progress 40% @chr7:43000001, elapsed 0.3s, est remaining 0.4s, peak mem 101MB, user 0.6s, sys 7.7s, output queue size 12
progress 45% @chr8:43000001, elapsed 0.3s, est remaining 0.4s, peak mem 101MB, user 0.7s, sys 8.6s, output queue size 14
progress 50% @chr9:65000001, elapsed 0.4s, est remaining 0.4s, peak mem 101MB, user 0.8s, sys 9.6s, output queue size 9
progress 55% @chr10:92000001, elapsed 0.4s, est remaining 0.3s, peak mem 101MB, user 0.8s, sys 10.7s, output queue size 7
progress 60% @chr11:112000001, elapsed 0.4s, est remaining 0.3s, peak mem 101MB, user 0.9s, sys 11.6s, output queue size 11
progress 65% @chr13:7000001, elapsed 0.5s, est remaining 0.2s, peak mem 101MB, user 1.0s, sys 12.6s, output queue size 8
progress 70% @chr14:54000001, elapsed 0.5s, est remaining 0.2s, peak mem 101MB, user 1.1s, sys 13.6s, output queue size 7
progress 75% @chr16:29000001, elapsed 0.5s, est remaining 0.2s, peak mem 101MB, user 1.2s, sys 14.5s, output queue size 8
progress 80% @chr17:79000001, elapsed 0.6s, est remaining 0.1s, peak mem 101MB, user 1.3s, sys 15.5s, output queue size 8
progress 85% @chr20:14000001, elapsed 0.6s, est remaining 0.1s, peak mem 101MB, user 1.4s, sys 16.5s, output queue size 9
progress 90% @chrX:45000001, elapsed 0.7s, est remaining 0.1s, peak mem 143MB, user 1.9s, sys 17.0s, output queue size 114
progress 95% @chrY:34000001, elapsed 0.7s, est remaining 0.0s, peak mem 161MB, user 2.5s, sys 17.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.3s, est remaining 0.0s, peak mem 178MB, user 4.3s, sys 18.8s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 51395349
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.850 user 9.817 sys 11.666 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 0.001 user 0.001 sys 1.323 real
idle: 82 calls 0.011 user 0.027 sys 47.590 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 187396096 mem 4.549 user 19.653 sys 2.505 real