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/71/a2cf253a3b935f5fb7056edc777d2d/.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/71/a2cf253a3b935f5fb7056edc777d2d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/6deb667df284430001177d0a9637ad/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/6deb667df284430001177d0a9637ad/HCC1395_tumor.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_tumor.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_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:152000001, elapsed 0.0s, est remaining 0.8s, peak mem 93MB, user 0.1s, sys 0.8s, output queue size 13
progress 10% @chr2:66000001, elapsed 0.1s, est remaining 1.0s, peak mem 93MB, user 0.2s, sys 2.6s, output queue size 33
progress 15% @chr3:20000001, elapsed 0.2s, est remaining 1.0s, peak mem 93MB, user 0.3s, sys 4.7s, output queue size 30
progress 20% @chr3:180000001, elapsed 0.3s, est remaining 1.0s, peak mem 93MB, user 0.4s, sys 6.8s, output queue size 12
progress 25% @chr4:143000001, elapsed 0.3s, est remaining 1.0s, peak mem 93MB, user 0.5s, sys 8.9s, output queue size 58
progress 30% @chr5:78000001, elapsed 0.4s, est remaining 0.9s, peak mem 93MB, user 0.6s, sys 11.0s, output queue size 36
progress 35% @chr6:57000001, elapsed 0.5s, est remaining 0.9s, peak mem 93MB, user 0.7s, sys 13.1s, output queue size 10
progress 40% @chr7:46000001, elapsed 0.5s, est remaining 0.8s, peak mem 93MB, user 0.8s, sys 15.1s, output queue size 33
progress 45% @chr8:44000001, elapsed 0.6s, est remaining 0.7s, peak mem 93MB, user 0.9s, sys 17.2s, output queue size 28
progress 50% @chr9:63000001, elapsed 0.7s, est remaining 0.7s, peak mem 93MB, user 1.0s, sys 19.3s, output queue size 25
progress 55% @chr10:85000001, elapsed 0.8s, est remaining 0.6s, peak mem 93MB, user 1.1s, sys 21.5s, output queue size 16
progress 60% @chr11:114000001, elapsed 0.8s, est remaining 0.5s, peak mem 93MB, user 1.2s, sys 23.6s, output queue size 17
progress 65% @chr13:3000001, elapsed 0.9s, est remaining 0.5s, peak mem 93MB, user 1.3s, sys 25.7s, output queue size 51
progress 70% @chr14:54000001, elapsed 1.0s, est remaining 0.4s, peak mem 93MB, user 1.5s, sys 27.8s, output queue size 22
progress 75% @chr15:99000001, elapsed 1.0s, est remaining 0.3s, peak mem 93MB, user 1.6s, sys 29.9s, output queue size 21
progress 80% @chr18:24000001, elapsed 1.1s, est remaining 0.3s, peak mem 93MB, user 1.7s, sys 32.4s, output queue size 16
progress 85% @chr20:4000001, elapsed 1.2s, est remaining 0.2s, peak mem 93MB, user 1.7s, sys 34.7s, output queue size 18
progress 90% @chrX:34000001, elapsed 1.3s, est remaining 0.1s, peak mem 102MB, user 2.2s, sys 35.9s, output queue size 114
progress 95% @chrY:30000001, elapsed 1.4s, est remaining 0.1s, peak mem 111MB, user 2.6s, sys 37.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.9s, est remaining 0.0s, peak mem 141MB, user 4.0s, sys 41.0s, 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: 50813895
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.329 user 21.492 sys 22.935 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 1.918 real
idle: 74 calls 0.003 user 0.015 sys 43.967 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 147947520 mem 4.200 user 41.656 sys 3.083 real