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/4d/b9e144414462a8174ec4d84af41155/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
  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/4d/b9e144414462a8174ec4d84af41155/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/affe90ad272751a557cfb55ea8a87a/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/affe90ad272751a557cfb55ea8a87a/HCC1395_tumor.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_tumor.md.bam --algo HsMetricAlgo --targets_list targets/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.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_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:144000001, elapsed 0.1s, est remaining 1.3s, peak mem 111MB, user 1.3s, sys 0.2s, output queue size 17
progress 10% @chr2:55000001, elapsed 0.1s, est remaining 1.1s, peak mem 111MB, user 2.9s, sys 0.4s, output queue size 18
progress 15% @chr2:222000001, elapsed 0.2s, est remaining 1.0s, peak mem 111MB, user 4.3s, sys 0.9s, output queue size 21
progress 20% @chr3:143000001, elapsed 0.2s, est remaining 1.0s, peak mem 111MB, user 5.6s, sys 1.4s, output queue size 25
progress 25% @chr4:104000001, elapsed 0.3s, est remaining 0.9s, peak mem 111MB, user 6.7s, sys 2.1s, output queue size 33
progress 30% @chr5:76000001, elapsed 0.4s, est remaining 0.8s, peak mem 111MB, user 8.2s, sys 2.4s, output queue size 43
progress 35% @chr6:83000001, elapsed 0.4s, est remaining 0.8s, peak mem 111MB, user 9.8s, sys 2.6s, output queue size 48
progress 40% @chr7:42000001, elapsed 0.5s, est remaining 0.7s, peak mem 111MB, user 11.4s, sys 3.0s, output queue size 16
progress 45% @chr8:84000001, elapsed 0.5s, est remaining 0.7s, peak mem 111MB, user 12.5s, sys 3.6s, output queue size 29
progress 50% @chr9:60000001, elapsed 0.6s, est remaining 0.6s, peak mem 111MB, user 13.7s, sys 4.2s, output queue size 40
progress 55% @chr10:80000001, elapsed 0.7s, est remaining 0.5s, peak mem 111MB, user 15.3s, sys 4.4s, output queue size 45
progress 60% @chr11:108000001, elapsed 0.7s, est remaining 0.5s, peak mem 111MB, user 16.6s, sys 4.9s, output queue size 27
progress 65% @chr13:39000001, elapsed 0.8s, est remaining 0.4s, peak mem 111MB, user 18.1s, sys 5.1s, output queue size 28
progress 70% @chr14:79000001, elapsed 0.8s, est remaining 0.4s, peak mem 111MB, user 19.7s, sys 5.4s, output queue size 35
progress 75% @chr16:33000001, elapsed 0.9s, est remaining 0.3s, peak mem 111MB, user 21.2s, sys 5.6s, output queue size 44
progress 80% @chr17:70000001, elapsed 0.9s, est remaining 0.2s, peak mem 111MB, user 22.8s, sys 5.9s, output queue size 29
progress 85% @chr20:2000001, elapsed 1.0s, est remaining 0.2s, peak mem 111MB, user 24.2s, sys 6.2s, output queue size 56
progress 90% @chrX:29000001, elapsed 1.1s, est remaining 0.1s, peak mem 120MB, user 25.0s, sys 7.3s, output queue size 114
progress 95% @chrY:50000001, elapsed 1.2s, est remaining 0.1s, peak mem 123MB, user 25.5s, sys 8.7s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.7s, est remaining 0.0s, peak mem 159MB, user 27.3s, sys 11.6s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50813903
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.909 user 6.373 sys 8.504 real
done: 1 calls 0.007 user 0.000 sys 0.011 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.003 sys 1.735 real
idle: 83 calls 0.020 user 0.008 sys 44.550 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 166809600 mem 28.106 user 11.995 sys 3.257 real