Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/9bc2477a071584c0387d1c6464c441/HCC1395_BL.md.bam
  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/02/c7c7d7af5300961658db694596c2bc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/c7c7d7af5300961658db694596c2bc/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/9bc2477a071584c0387d1c6464c441/HCC1395_BL.md.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i HCC1395_BL.md.bam --algo AlignmentStat HCC1395_BL.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo HCC1395_BL.sentieon.insert_size_metrics --algo QualDistribution HCC1395_BL.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle HCC1395_BL.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle HCC1395_BL.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 0.0s, est remaining 0.5s, peak mem 81MB, user 0.1s, sys 0.3s, output queue size 3
progress 10% @chr2:72000001, elapsed 0.0s, est remaining 0.4s, peak mem 81MB, user 0.1s, sys 0.9s, output queue size 1
progress 15% @chr2:232000001, elapsed 0.1s, est remaining 0.4s, peak mem 81MB, user 0.2s, sys 1.4s, output queue size 3
progress 20% @chr3:152000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.3s, sys 1.9s, output queue size 9
progress 25% @chr4:115000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.4s, sys 2.4s, output queue size 1
progress 30% @chr5:86000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.5s, sys 3.0s, output queue size 27
progress 35% @chr6:66000001, elapsed 0.1s, est remaining 0.3s, peak mem 81MB, user 0.5s, sys 3.6s, output queue size 18
progress 40% @chr7:55000001, elapsed 0.2s, est remaining 0.3s, peak mem 81MB, user 0.6s, sys 4.2s, output queue size 16
progress 45% @chr8:56000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.7s, sys 4.8s, output queue size 1
progress 50% @chr9:72000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.8s, sys 5.3s, output queue size 1
progress 55% @chr10:94000001, elapsed 0.2s, est remaining 0.2s, peak mem 81MB, user 0.9s, sys 5.9s, output queue size 7
progress 60% @chr11:122000001, elapsed 0.3s, est remaining 0.2s, peak mem 81MB, user 0.9s, sys 6.5s, output queue size 2
progress 65% @chr12:129000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.0s, sys 7.1s, output queue size 20
progress 70% @chr14:62000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.0s, sys 7.6s, output queue size 20
progress 75% @chr16:14000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.1s, sys 8.1s, output queue size 17
progress 80% @chr18:2000001, elapsed 0.3s, est remaining 0.1s, peak mem 81MB, user 1.2s, sys 8.6s, output queue size 14
progress 85% @chr20:23000001, elapsed 0.4s, est remaining 0.1s, peak mem 81MB, user 1.2s, sys 9.2s, output queue size 8
progress 90% @chrX:44000001, elapsed 0.4s, est remaining 0.0s, peak mem 105MB, user 1.6s, sys 9.4s, output queue size 114
progress 95% @chrY:40000001, elapsed 0.4s, est remaining 0.0s, peak mem 129MB, user 2.3s, sys 9.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.1s, est remaining 0.0s, peak mem 168MB, user 5.2s, sys 9.9s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 51394930
reads: 1001089
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.196 user 4.840 sys 6.517 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 0.001 user 0.002 sys 1.158 real
idle: 74 calls 0.034 user 0.031 sys 50.505 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 176431104 mem 5.513 user 10.539 sys 2.202 real