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/97/2c6b5990e9a11787cfd337594154c5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/2c6b5990e9a11787cfd337594154c5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/6f66ca245d08590522a343bbd58529/HCC1395_tumor.md.bam
  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/9d/6f66ca245d08590522a343bbd58529/HCC1395_tumor.md.bam.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i HCC1395_tumor.md.bam --algo AlignmentStat HCC1395_tumor.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo HCC1395_tumor.sentieon.insert_size_metrics --algo QualDistribution HCC1395_tumor.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle HCC1395_tumor.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle HCC1395_tumor.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:164000001, elapsed 0.0s, est remaining 0.7s, peak mem 81MB, user 0.1s, sys 0.8s, output queue size 12
progress 10% @chr2:74000001, elapsed 0.1s, est remaining 0.7s, peak mem 81MB, user 0.2s, sys 1.7s, output queue size 20
progress 15% @chr2:235000001, elapsed 0.1s, est remaining 0.6s, peak mem 81MB, user 0.3s, sys 2.6s, output queue size 23
progress 20% @chr3:152000001, elapsed 0.1s, est remaining 0.6s, peak mem 81MB, user 0.3s, sys 3.7s, output queue size 1
progress 25% @chr4:118000001, elapsed 0.2s, est remaining 0.5s, peak mem 81MB, user 0.4s, sys 4.5s, output queue size 5
progress 30% @chr5:87000001, elapsed 0.2s, est remaining 0.5s, peak mem 81MB, user 0.5s, sys 5.5s, output queue size 4
progress 35% @chr6:63000001, elapsed 0.2s, est remaining 0.4s, peak mem 81MB, user 0.6s, sys 6.4s, output queue size 2
progress 40% @chr7:57000001, elapsed 0.3s, est remaining 0.4s, peak mem 81MB, user 0.7s, sys 7.2s, output queue size 5
progress 45% @chr8:53000001, elapsed 0.3s, est remaining 0.4s, peak mem 81MB, user 0.9s, sys 8.1s, output queue size 4
progress 50% @chr9:67000001, elapsed 0.3s, est remaining 0.3s, peak mem 81MB, user 1.0s, sys 9.0s, output queue size 6
progress 55% @chr10:96000001, elapsed 0.4s, est remaining 0.3s, peak mem 81MB, user 1.0s, sys 9.9s, output queue size 8
progress 60% @chr11:122000001, elapsed 0.4s, est remaining 0.3s, peak mem 81MB, user 1.2s, sys 10.7s, output queue size 3
progress 65% @chr13:14000001, elapsed 0.4s, est remaining 0.2s, peak mem 81MB, user 1.3s, sys 11.7s, output queue size 1
progress 70% @chr14:62000001, elapsed 0.5s, est remaining 0.2s, peak mem 81MB, user 1.5s, sys 12.5s, output queue size 2
progress 75% @chr16:12000001, elapsed 0.5s, est remaining 0.2s, peak mem 81MB, user 1.6s, sys 13.4s, output queue size 1
progress 80% @chr17:81000001, elapsed 0.5s, est remaining 0.1s, peak mem 81MB, user 1.7s, sys 14.2s, output queue size 4
progress 85% @chr20:20000001, elapsed 0.6s, est remaining 0.1s, peak mem 81MB, user 1.9s, sys 15.1s, output queue size 2
progress 90% @chrX:41000001, elapsed 0.6s, est remaining 0.1s, peak mem 96MB, user 2.5s, sys 15.5s, output queue size 114
progress 95% @chrY:37000001, elapsed 0.7s, est remaining 0.0s, peak mem 111MB, user 3.2s, sys 15.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.4s, est remaining 0.0s, peak mem 132MB, user 6.2s, sys 16.8s, 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: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 50813904
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.162 user 8.377 sys 9.919 real
done: 1 calls 0.000 user 0.000 sys 0.001 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.003 sys 1.406 real
idle: 78 calls 0.019 user 0.019 sys 50.191 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 138477568 mem 6.407 user 17.401 sys 2.448 real