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/14/cb9b4fd67ef158ec3e5d2b7b71b4d0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/1522a57805e7cad4bff5ff92b93eac/Sig_18_tissue.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_footprint.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/14/cb9b4fd67ef158ec3e5d2b7b71b4d0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/1522a57805e7cad4bff5ff92b93eac/Sig_18_tissue.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
==> STAGING COMPLETE (8 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i Sig_18_tissue.md.bam --algo HsMetricAlgo --targets_list targets/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed --baits_list baits/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed Sig_18_tissue_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:150000001, elapsed 0.0s, est remaining 0.5s, peak mem 120MB, user 0.1s, sys 0.3s, output queue size 11
progress 10% @chr2:64000001, elapsed 0.0s, est remaining 0.4s, peak mem 120MB, user 0.2s, sys 0.9s, output queue size 9
progress 15% @chr2:238000001, elapsed 0.1s, est remaining 0.4s, peak mem 120MB, user 0.3s, sys 1.4s, output queue size 9
progress 20% @chr3:157000001, elapsed 0.1s, est remaining 0.4s, peak mem 120MB, user 0.4s, sys 2.0s, output queue size 10
progress 25% @chr4:122000001, elapsed 0.1s, est remaining 0.3s, peak mem 120MB, user 0.5s, sys 2.6s, output queue size 11
progress 30% @chr5:86000001, elapsed 0.1s, est remaining 0.3s, peak mem 120MB, user 0.6s, sys 3.2s, output queue size 3
progress 35% @chr6:72000001, elapsed 0.2s, est remaining 0.3s, peak mem 120MB, user 0.6s, sys 3.8s, output queue size 11
progress 40% @chr7:46000001, elapsed 0.2s, est remaining 0.3s, peak mem 120MB, user 0.7s, sys 4.3s, output queue size 10
progress 45% @chr8:63000001, elapsed 0.2s, est remaining 0.2s, peak mem 120MB, user 0.8s, sys 4.9s, output queue size 7
progress 50% @chr9:79000001, elapsed 0.2s, est remaining 0.2s, peak mem 120MB, user 0.9s, sys 5.6s, output queue size 11
progress 55% @chr10:93000001, elapsed 0.2s, est remaining 0.2s, peak mem 120MB, user 1.0s, sys 6.1s, output queue size 10
progress 60% @chr11:120000001, elapsed 0.3s, est remaining 0.2s, peak mem 120MB, user 1.0s, sys 6.7s, output queue size 14
progress 65% @chr13:21000001, elapsed 0.3s, est remaining 0.2s, peak mem 121MB, user 1.1s, sys 7.2s, output queue size 5
progress 70% @chr14:71000001, elapsed 0.3s, est remaining 0.1s, peak mem 121MB, user 1.2s, sys 7.8s, output queue size 15
progress 75% @chr16:18000001, elapsed 0.3s, est remaining 0.1s, peak mem 121MB, user 1.3s, sys 8.4s, output queue size 6
progress 80% @chr18:3000001, elapsed 0.4s, est remaining 0.1s, peak mem 121MB, user 1.4s, sys 8.9s, output queue size 10
progress 85% @chr20:13000001, elapsed 0.4s, est remaining 0.1s, peak mem 121MB, user 1.6s, sys 9.5s, output queue size 9
progress 90% @chrX:44000001, elapsed 0.4s, est remaining 0.0s, peak mem 162MB, user 1.9s, sys 9.6s, output queue size 114
progress 95% @chrY:45000001, elapsed 0.4s, est remaining 0.0s, peak mem 180MB, user 2.1s, sys 9.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.3s, est remaining 0.0s, peak mem 199MB, user 5.2s, sys 10.1s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 64
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50047062
reads: 1001838
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.660 user 5.116 sys 7.071 real
done: 1 calls 0.002 user 0.000 sys 0.010 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.001 sys 1.347 real
idle: 72 calls 0.033 user 0.053 sys 56.434 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 210489344 mem 5.915 user 10.836 sys 3.001 real