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/3b/2d024735f3e3bc206010d35ee519b7/.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-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_postQC_hg38.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/2d024735f3e3bc206010d35ee519b7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/de14d1288827a7d870211563ddef46/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/de14d1288827a7d870211563ddef46/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/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_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:174000001, elapsed 0.1s, est remaining 1.3s, peak mem 99MB, user 0.2s, sys 1.4s, output queue size 15
progress 10% @chr2:63000001, elapsed 0.1s, est remaining 1.2s, peak mem 99MB, user 0.5s, sys 3.0s, output queue size 13
progress 15% @chr2:226000001, elapsed 0.2s, est remaining 1.1s, peak mem 99MB, user 0.7s, sys 4.7s, output queue size 10
progress 20% @chr3:143000001, elapsed 0.2s, est remaining 1.0s, peak mem 99MB, user 0.7s, sys 6.5s, output queue size 12
progress 25% @chr4:120000001, elapsed 0.3s, est remaining 0.9s, peak mem 99MB, user 0.8s, sys 8.3s, output queue size 12
progress 30% @chr5:75000001, elapsed 0.4s, est remaining 0.9s, peak mem 99MB, user 1.0s, sys 10.0s, output queue size 15
progress 35% @chr6:58000001, elapsed 0.4s, est remaining 0.8s, peak mem 99MB, user 1.0s, sys 11.7s, output queue size 7
progress 40% @chr7:62000001, elapsed 0.5s, est remaining 0.7s, peak mem 99MB, user 1.1s, sys 13.5s, output queue size 9
progress 45% @chr8:49000001, elapsed 0.6s, est remaining 0.7s, peak mem 99MB, user 1.3s, sys 15.2s, output queue size 14
progress 50% @chr9:77000001, elapsed 0.6s, est remaining 0.6s, peak mem 99MB, user 1.4s, sys 17.0s, output queue size 4
progress 55% @chr10:100000001, elapsed 0.7s, est remaining 0.6s, peak mem 99MB, user 1.5s, sys 18.7s, output queue size 7
progress 60% @chr11:125000001, elapsed 0.7s, est remaining 0.5s, peak mem 99MB, user 1.7s, sys 20.4s, output queue size 12
progress 65% @chr13:3000001, elapsed 0.8s, est remaining 0.4s, peak mem 99MB, user 1.8s, sys 22.2s, output queue size 12
progress 70% @chr14:52000001, elapsed 0.9s, est remaining 0.4s, peak mem 99MB, user 1.9s, sys 23.9s, output queue size 9
progress 75% @chr16:18000001, elapsed 0.9s, est remaining 0.3s, peak mem 99MB, user 2.0s, sys 25.7s, output queue size 7
progress 80% @chr18:7000001, elapsed 1.0s, est remaining 0.2s, peak mem 99MB, user 2.0s, sys 27.5s, output queue size 10
progress 85% @chr20:11000001, elapsed 1.0s, est remaining 0.2s, peak mem 99MB, user 2.2s, sys 29.2s, output queue size 11
progress 90% @chrX:37000001, elapsed 1.1s, est remaining 0.1s, peak mem 99MB, user 2.7s, sys 30.4s, output queue size 114
progress 95% @chrY:17000001, elapsed 1.2s, est remaining 0.1s, peak mem 114MB, user 3.1s, sys 32.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.7s, est remaining 0.0s, peak mem 147MB, user 4.4s, sys 34.9s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 50813900
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.284 user 18.288 sys 19.836 real
done: 1 calls 0.000 user 0.002 sys 0.006 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.002 sys 1.705 real
idle: 81 calls 0.005 user 0.018 sys 42.957 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 154234880 mem 4.676 user 35.565 sys 2.877 real