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/d9/3b27f07a2dd31f8328c65dd72a40a8/.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/d9/3b27f07a2dd31f8328c65dd72a40a8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/b9a654c2eb185e6f039bc9f9968f2d/HCC1395_tumor.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/b9a654c2eb185e6f039bc9f9968f2d/HCC1395_tumor.md.bam
  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
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.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_minus_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_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_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 112MB, user 0.1s, sys 0.5s, output queue size 28
progress 10% @chr2:75000001, elapsed 0.1s, est remaining 0.5s, peak mem 112MB, user 0.2s, sys 1.2s, output queue size 17
progress 15% @chr2:234000001, elapsed 0.1s, est remaining 0.5s, peak mem 112MB, user 0.3s, sys 1.9s, output queue size 11
progress 20% @chr3:156000001, elapsed 0.1s, est remaining 0.4s, peak mem 112MB, user 0.3s, sys 2.7s, output queue size 17
progress 25% @chr4:116000001, elapsed 0.1s, est remaining 0.4s, peak mem 112MB, user 0.4s, sys 3.4s, output queue size 26
progress 30% @chr5:86000001, elapsed 0.2s, est remaining 0.4s, peak mem 112MB, user 0.5s, sys 4.1s, output queue size 11
progress 35% @chr6:65000001, elapsed 0.2s, est remaining 0.3s, peak mem 112MB, user 0.5s, sys 4.9s, output queue size 1
progress 40% @chr7:58000001, elapsed 0.2s, est remaining 0.3s, peak mem 112MB, user 0.6s, sys 5.5s, output queue size 30
progress 45% @chr8:58000001, elapsed 0.2s, est remaining 0.3s, peak mem 112MB, user 0.8s, sys 6.2s, output queue size 4
progress 50% @chr9:73000001, elapsed 0.3s, est remaining 0.3s, peak mem 112MB, user 0.8s, sys 6.8s, output queue size 34
progress 55% @chr10:94000001, elapsed 0.3s, est remaining 0.2s, peak mem 112MB, user 0.9s, sys 7.6s, output queue size 11
progress 60% @chr11:122000001, elapsed 0.3s, est remaining 0.2s, peak mem 112MB, user 1.0s, sys 8.2s, output queue size 12
progress 65% @chr13:19000001, elapsed 0.3s, est remaining 0.2s, peak mem 112MB, user 1.1s, sys 8.9s, output queue size 19
progress 70% @chr14:64000001, elapsed 0.4s, est remaining 0.2s, peak mem 112MB, user 1.1s, sys 9.5s, output queue size 3
progress 75% @chr16:13000001, elapsed 0.4s, est remaining 0.1s, peak mem 112MB, user 1.2s, sys 10.3s, output queue size 25
progress 80% @chr18:1000001, elapsed 0.4s, est remaining 0.1s, peak mem 112MB, user 1.2s, sys 10.9s, output queue size 10
progress 85% @chr20:22000001, elapsed 0.4s, est remaining 0.1s, peak mem 112MB, user 1.3s, sys 11.6s, output queue size 11
progress 90% @chrX:37000001, elapsed 0.5s, est remaining 0.1s, peak mem 144MB, user 1.7s, sys 12.0s, output queue size 114
progress 95% @chrY:36000001, elapsed 0.5s, est remaining 0.0s, peak mem 157MB, user 2.0s, sys 12.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 0.8s, est remaining 0.0s, peak mem 181MB, user 3.4s, sys 13.5s, 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: 50813899
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.126 user 6.788 sys 8.381 real
done: 1 calls 0.000 user 0.000 sys 0.007 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.002 sys 0.825 real
idle: 73 calls 0.008 user 0.018 sys 38.379 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 190603264 mem 3.856 user 14.380 sys 2.281 real