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/fe/404e2e82af49022f34826881eef9d9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/404e2e82af49022f34826881eef9d9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/3eec84bf4a6278923d178da5170ede/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/fa/3eec84bf4a6278923d178da5170ede/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% @chr1:152000001, elapsed 0.0s, est remaining 0.6s, peak mem 81MB, user 0.1s, sys 0.5s, output queue size 9
progress 10% @chr2:76000001, elapsed 0.1s, est remaining 0.5s, peak mem 81MB, user 0.2s, sys 1.3s, output queue size 13
progress 15% @chr2:239000001, elapsed 0.1s, est remaining 0.5s, peak mem 81MB, user 0.3s, sys 2.0s, output queue size 15
progress 20% @chr3:154000001, elapsed 0.1s, est remaining 0.5s, peak mem 81MB, user 0.3s, sys 2.7s, output queue size 18
progress 25% @chr4:116000001, elapsed 0.1s, est remaining 0.4s, peak mem 81MB, user 0.4s, sys 3.6s, output queue size 2
progress 30% @chr5:85000001, elapsed 0.2s, est remaining 0.4s, peak mem 81MB, user 0.5s, sys 4.4s, output queue size 4
progress 35% @chr6:70000001, elapsed 0.2s, est remaining 0.4s, peak mem 81MB, user 0.6s, sys 4.9s, output queue size 25
progress 40% @chr7:36000001, elapsed 0.2s, est remaining 0.3s, peak mem 81MB, user 0.7s, sys 5.7s, output queue size 19
progress 45% @chr8:60000001, elapsed 0.2s, est remaining 0.3s, peak mem 81MB, user 0.7s, sys 6.4s, output queue size 9
progress 50% @chr9:66000001, elapsed 0.3s, est remaining 0.3s, peak mem 81MB, user 0.8s, sys 7.1s, output queue size 7
progress 55% @chr10:96000001, elapsed 0.3s, est remaining 0.2s, peak mem 81MB, user 0.9s, sys 7.9s, output queue size 10
progress 60% @chr11:123000001, elapsed 0.3s, est remaining 0.2s, peak mem 81MB, user 1.0s, sys 8.4s, output queue size 13
progress 65% @chr13:16000001, elapsed 0.3s, est remaining 0.2s, peak mem 81MB, user 1.1s, sys 9.2s, output queue size 7
progress 70% @chr14:61000001, elapsed 0.4s, est remaining 0.2s, peak mem 81MB, user 1.2s, sys 9.8s, output queue size 5
progress 75% @chr16:14000001, elapsed 0.4s, est remaining 0.1s, peak mem 81MB, user 1.2s, sys 10.6s, output queue size 14
progress 80% @chr18:1, elapsed 0.4s, est remaining 0.1s, peak mem 81MB, user 1.3s, sys 11.5s, output queue size 3
progress 85% @chr20:23000001, elapsed 0.5s, est remaining 0.1s, peak mem 81MB, user 1.3s, sys 12.2s, output queue size 4
progress 90% @chrX:42000001, elapsed 0.5s, est remaining 0.1s, peak mem 108MB, user 1.8s, sys 12.5s, output queue size 114
progress 95% @chrY:38000001, elapsed 0.6s, est remaining 0.0s, peak mem 124MB, user 2.5s, sys 13.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.3s, est remaining 0.0s, peak mem 156MB, user 5.4s, sys 13.6s, 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: 50815332
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.102 user 6.498 sys 8.287 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 0.001 sys 1.365 real
idle: 72 calls 0.033 user 0.022 sys 52.855 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 163872768 mem 5.636 user 14.297 sys 2.416 real