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/e1/c09a41c22663150297319fd22a354a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/a9e2ccd0c8e1b97d551b9ee4f0aee5/Sig_18_tissue.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/c09a41c22663150297319fd22a354a/.command.run
  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/f5/a9e2ccd0c8e1b97d551b9ee4f0aee5/Sig_18_tissue.md.bam
==> STAGING COMPLETE (6 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 AlignmentStat Sig_18_tissue.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo Sig_18_tissue.sentieon.insert_size_metrics --algo QualDistribution Sig_18_tissue.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle Sig_18_tissue.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle Sig_18_tissue.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
progress 5% @chr1:172000001, elapsed 600.1s, est remaining 11402.6s, peak mem 81MB, user 0.1s, sys 0.1s, output queue size 113
progress 10% @chr2:69000001, elapsed 600.2s, est remaining 5401.6s, peak mem 81MB, user 0.2s, sys 0.6s, output queue size 270
progress 15% @chr2:236000001, elapsed 600.2s, est remaining 3401.3s, peak mem 81MB, user 0.3s, sys 1.5s, output queue size 18
progress 20% @chr3:128000001, elapsed 600.3s, est remaining 2401.1s, peak mem 81MB, user 0.4s, sys 3.0s, output queue size 25
progress 25% @chr4:116000001, elapsed 600.3s, est remaining 1801.0s, peak mem 81MB, user 0.6s, sys 4.3s, output queue size 5
progress 30% @chr5:87000001, elapsed 600.4s, est remaining 1400.9s, peak mem 81MB, user 0.7s, sys 5.7s, output queue size 1
progress 35% @chr6:65000001, elapsed 600.4s, est remaining 1115.1s, peak mem 81MB, user 0.9s, sys 7.1s, output queue size 1
progress 40% @chr7:53000001, elapsed 600.5s, est remaining 900.8s, peak mem 81MB, user 1.1s, sys 8.7s, output queue size 2
progress 45% @chr8:59000001, elapsed 600.6s, est remaining 734.0s, peak mem 81MB, user 1.2s, sys 10.3s, output queue size 1
progress 50% @chr9:70000001, elapsed 600.6s, est remaining 600.6s, peak mem 81MB, user 1.3s, sys 11.9s, output queue size 3
progress 55% @chr10:95000001, elapsed 600.7s, est remaining 491.5s, peak mem 81MB, user 1.4s, sys 13.4s, output queue size 5
progress 60% @chr11:121000001, elapsed 600.7s, est remaining 400.5s, peak mem 81MB, user 1.5s, sys 15.0s, output queue size 2
progress 65% @chr13:16000001, elapsed 600.8s, est remaining 323.5s, peak mem 81MB, user 1.6s, sys 16.6s, output queue size 1
progress 70% @chr14:61000001, elapsed 600.8s, est remaining 257.5s, peak mem 81MB, user 1.7s, sys 18.2s, output queue size 15
progress 75% @chr16:9000001, elapsed 600.9s, est remaining 200.3s, peak mem 81MB, user 1.8s, sys 19.7s, output queue size 4
progress 80% @chr18:1, elapsed 601.0s, est remaining 150.2s, peak mem 81MB, user 1.9s, sys 21.2s, output queue size 2
progress 85% @chr20:20000001, elapsed 601.0s, est remaining 106.1s, peak mem 81MB, user 2.1s, sys 22.7s, output queue size 3
progress 90% @chrX:43000001, elapsed 601.1s, est remaining 66.8s, peak mem 114MB, user 2.7s, sys 23.4s, output queue size 114
progress 95% @chrY:40000001, elapsed 601.2s, est remaining 31.6s, peak mem 129MB, user 3.6s, sys 24.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 602.3s, est remaining 0.0s, peak mem 154MB, user 8.1s, sys 25.5s, 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: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 50047064
reads: 1001838
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.660 user 12.348 sys 16.037 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.003 sys 602.382 real
idle: 89 calls 0.020 user 0.017 sys 64.065 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 162234368 mem 8.364 user 26.909 sys 603.458 real