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/4b/9422dcbf81219187331d9bda16cc4b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/9422dcbf81219187331d9bda16cc4b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/1b780e82228e825cb40abaea84a098/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/ef/1b780e82228e825cb40abaea84a098/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.
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% @chr1:150000001, elapsed 240.1s, est remaining 4561.4s, peak mem 81MB, user 0.2s, sys 0.3s, output queue size 17
progress 10% @chr2:59000001, elapsed 240.1s, est remaining 2160.9s, peak mem 81MB, user 0.5s, sys 0.8s, output queue size 14
progress 15% @chr3:1000001, elapsed 240.1s, est remaining 1360.7s, peak mem 81MB, user 0.7s, sys 1.3s, output queue size 10
progress 20% @chr3:158000001, elapsed 240.1s, est remaining 960.6s, peak mem 81MB, user 0.9s, sys 1.6s, output queue size 12
progress 25% @chr4:122000001, elapsed 240.2s, est remaining 720.5s, peak mem 81MB, user 1.1s, sys 2.2s, output queue size 11
progress 30% @chr5:90000001, elapsed 240.2s, est remaining 560.4s, peak mem 81MB, user 1.3s, sys 2.7s, output queue size 11
progress 35% @chr6:62000001, elapsed 240.2s, est remaining 446.1s, peak mem 81MB, user 1.5s, sys 3.2s, output queue size 13
progress 40% @chr7:48000001, elapsed 240.2s, est remaining 360.4s, peak mem 81MB, user 1.6s, sys 3.7s, output queue size 13
progress 45% @chr8:41000001, elapsed 240.3s, est remaining 293.6s, peak mem 82MB, user 1.8s, sys 4.3s, output queue size 16
progress 50% @chr9:57000001, elapsed 240.3s, est remaining 240.3s, peak mem 82MB, user 2.1s, sys 4.7s, output queue size 16
progress 55% @chr10:85000001, elapsed 240.3s, est remaining 196.6s, peak mem 82MB, user 2.2s, sys 5.2s, output queue size 10
progress 60% @chr11:129000001, elapsed 240.3s, est remaining 160.2s, peak mem 82MB, user 2.3s, sys 5.7s, output queue size 21
progress 65% @chr13:20000001, elapsed 240.3s, est remaining 129.4s, peak mem 82MB, user 2.7s, sys 6.0s, output queue size 12
progress 70% @chr14:64000001, elapsed 240.4s, est remaining 103.0s, peak mem 82MB, user 2.8s, sys 6.6s, output queue size 17
progress 75% @chr16:16000001, elapsed 240.4s, est remaining 80.1s, peak mem 82MB, user 2.9s, sys 7.2s, output queue size 29
progress 80% @chr17:81000001, elapsed 240.4s, est remaining 60.1s, peak mem 82MB, user 3.0s, sys 7.7s, output queue size 22
progress 85% @chr19:57000001, elapsed 240.4s, est remaining 42.4s, peak mem 82MB, user 3.1s, sys 8.2s, output queue size 24
progress 90% @chrX:43000001, elapsed 240.5s, est remaining 26.7s, peak mem 105MB, user 3.6s, sys 8.4s, output queue size 114
progress 95% @chrY:37000001, elapsed 240.5s, est remaining 12.7s, peak mem 120MB, user 4.0s, sys 8.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 241.2s, est remaining 0.0s, peak mem 165MB, user 7.4s, sys 9.1s, 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: 50813910
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.314 user 4.327 sys 6.315 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 0.003 user 0.004 sys 241.221 real
idle: 61 calls 0.035 user 0.031 sys 49.460 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 173117440 mem 7.713 user 9.649 sys 242.259 real