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/59/3670ef51ce1fdb38d7dbe681449387/.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/59/3670ef51ce1fdb38d7dbe681449387/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/48e31ffd7e189eae543e1792f9c5e0/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/48e31ffd7e189eae543e1792f9c5e0/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
  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% @chr1:153000001, elapsed 0.0s, est remaining 0.5s, peak mem 114MB, user 0.0s, sys 0.3s, output queue size 8
progress 10% @chr2:64000001, elapsed 0.0s, est remaining 0.4s, peak mem 114MB, user 0.1s, sys 0.8s, output queue size 9
progress 15% @chr2:227000001, elapsed 0.1s, est remaining 0.4s, peak mem 114MB, user 0.1s, sys 1.4s, output queue size 8
progress 20% @chr3:146000001, elapsed 0.1s, est remaining 0.4s, peak mem 114MB, user 0.2s, sys 2.1s, output queue size 7
progress 25% @chr4:106000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.3s, sys 2.7s, output queue size 9
progress 30% @chr5:76000001, elapsed 0.1s, est remaining 0.3s, peak mem 114MB, user 0.3s, sys 3.2s, output queue size 10
progress 35% @chr6:58000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.4s, sys 3.8s, output queue size 7
progress 40% @chr7:68000001, elapsed 0.2s, est remaining 0.3s, peak mem 114MB, user 0.5s, sys 4.4s, output queue size 10
progress 45% @chr8:50000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.5s, sys 5.1s, output queue size 7
progress 50% @chr9:94000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.6s, sys 5.7s, output queue size 9
progress 55% @chr10:92000001, elapsed 0.2s, est remaining 0.2s, peak mem 114MB, user 0.6s, sys 6.2s, output queue size 8
progress 60% @chr11:116000001, elapsed 0.3s, est remaining 0.2s, peak mem 114MB, user 0.7s, sys 6.8s, output queue size 9
progress 65% @chr13:37000001, elapsed 0.3s, est remaining 0.2s, peak mem 114MB, user 0.8s, sys 7.3s, output queue size 7
progress 70% @chr14:56000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 0.8s, sys 8.0s, output queue size 9
progress 75% @chr16:25000001, elapsed 0.3s, est remaining 0.1s, peak mem 114MB, user 0.9s, sys 8.6s, output queue size 11
progress 80% @chr18:16000001, elapsed 0.4s, est remaining 0.1s, peak mem 114MB, user 1.0s, sys 9.1s, output queue size 9
progress 85% @chr20:14000001, elapsed 0.4s, est remaining 0.1s, peak mem 114MB, user 1.0s, sys 9.7s, output queue size 8
progress 90% @chrX:41000001, elapsed 0.4s, est remaining 0.0s, peak mem 141MB, user 1.3s, sys 10.0s, output queue size 114
progress 95% @chrY:35000001, elapsed 0.4s, est remaining 0.0s, peak mem 160MB, user 1.7s, sys 10.5s, output queue size 276
progress 100% @chr21:41000001, elapsed 0.7s, est remaining 0.0s, peak mem 184MB, user 3.2s, sys 11.2s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50813905
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.078 user 5.875 sys 7.212 real
done: 1 calls 0.005 user 0.000 sys 0.007 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.002 sys 0.742 real
idle: 62 calls 0.003 user 0.007 sys 38.185 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 193667072 mem 3.623 user 12.107 sys 2.246 real