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/ec/39c8d52c974665febf6fe4a0b22c88/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/5506df0a357cd11929604eb852eb91/Sig_18_tissue.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/39c8d52c974665febf6fe4a0b22c88/.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/c3/5506df0a357cd11929604eb852eb91/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.
progress 5% @chr1:162000001, elapsed 0.0s, est remaining 0.6s, peak mem 79MB, user 0.1s, sys 0.4s, output queue size 9
progress 10% @chr2:71000001, elapsed 0.1s, est remaining 0.5s, peak mem 79MB, user 0.1s, sys 1.2s, output queue size 41
progress 15% @chr2:233000001, elapsed 0.1s, est remaining 0.5s, peak mem 79MB, user 0.2s, sys 1.8s, output queue size 17
progress 20% @chr3:155000001, elapsed 0.1s, est remaining 0.4s, peak mem 79MB, user 0.3s, sys 2.5s, output queue size 20
progress 25% @chr4:116000001, elapsed 0.1s, est remaining 0.4s, peak mem 79MB, user 0.4s, sys 3.2s, output queue size 6
progress 30% @chr5:86000001, elapsed 0.2s, est remaining 0.4s, peak mem 79MB, user 0.5s, sys 3.9s, output queue size 4
progress 35% @chr6:50000001, elapsed 0.2s, est remaining 0.3s, peak mem 79MB, user 0.6s, sys 4.6s, output queue size 15
progress 40% @chr7:55000001, elapsed 0.2s, est remaining 0.3s, peak mem 79MB, user 0.7s, sys 5.1s, output queue size 2
progress 45% @chr8:58000001, elapsed 0.2s, est remaining 0.3s, peak mem 79MB, user 0.9s, sys 5.9s, output queue size 16
progress 50% @chr9:77000001, elapsed 0.3s, est remaining 0.3s, peak mem 79MB, user 0.9s, sys 6.7s, output queue size 8
progress 55% @chr10:98000001, elapsed 0.3s, est remaining 0.2s, peak mem 79MB, user 1.0s, sys 7.4s, output queue size 18
progress 60% @chr11:122000001, elapsed 0.3s, est remaining 0.2s, peak mem 79MB, user 1.1s, sys 8.1s, output queue size 9
progress 65% @chr13:6000001, elapsed 0.3s, est remaining 0.2s, peak mem 79MB, user 1.2s, sys 9.0s, output queue size 9
progress 70% @chr14:60000001, elapsed 0.4s, est remaining 0.2s, peak mem 79MB, user 1.3s, sys 9.8s, output queue size 9
progress 75% @chr16:13000001, elapsed 0.4s, est remaining 0.1s, peak mem 79MB, user 1.4s, sys 10.6s, output queue size 5
progress 80% @chr18:2000001, elapsed 0.4s, est remaining 0.1s, peak mem 79MB, user 1.5s, sys 11.3s, output queue size 20
progress 85% @chr20:25000001, elapsed 0.5s, est remaining 0.1s, peak mem 79MB, user 1.6s, sys 12.1s, output queue size 15
progress 90% @chrX:44000001, elapsed 0.5s, est remaining 0.1s, peak mem 103MB, user 2.1s, sys 12.4s, output queue size 114
progress 95% @chrY:43000001, elapsed 0.6s, est remaining 0.0s, peak mem 118MB, user 2.7s, sys 12.7s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.3s, est remaining 0.0s, peak mem 150MB, user 6.0s, sys 13.2s, 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: 50047053
reads: 1001838
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.214 user 6.525 sys 8.125 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 0.002 user 0.001 sys 1.364 real
idle: 82 calls 0.028 user 0.040 sys 52.607 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 157573120 mem 6.308 user 13.767 sys 2.413 real