Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/5d2d2a40ebfadd6cf387c9473e6514/Sig_18_tissue.md.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/708452e2b2a5620be6748c4c9be7f5/Sig_18_tissue.table
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/5d2d2a40ebfadd6cf387c9473e6514/Sig_18_tissue.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/a4fe451521584478e1a5b710645b7f/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/a4fe451521584478e1a5b710645b7f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (13 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i Sig_18_tissue.md.bam --read_filter QualCalFilter,table=Sig_18_tissue.table,indel=false --algo QualCal -k dbsnp_146.hg38.vcf.gz -k Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -k Homo_sapiens_assembly38.known_indels.vcf.gz Sig_18_tissue.table.post --algo ReadWriter Sig_18_tissue.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:155000001, elapsed 0.1s, est remaining 2.2s, peak mem 416MB, user 0.3s, sys 2.7s, output queue size 16
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 1.9s, peak mem 776MB, user 0.6s, sys 5.5s, output queue size 19
progress 15% @chr2:236000001, elapsed 0.3s, est remaining 1.7s, peak mem 942MB, user 0.8s, sys 8.2s, output queue size 22
progress 20% @chr3:155000001, elapsed 0.4s, est remaining 1.6s, peak mem 1143MB, user 1.0s, sys 11.0s, output queue size 17
progress 25% @chr4:116000001, elapsed 0.5s, est remaining 1.5s, peak mem 1334MB, user 1.2s, sys 13.8s, output queue size 10
progress 30% @chr5:84000001, elapsed 0.6s, est remaining 1.4s, peak mem 1494MB, user 1.4s, sys 16.6s, output queue size 13
progress 35% @chr6:66000001, elapsed 0.7s, est remaining 1.3s, peak mem 1595MB, user 1.7s, sys 19.4s, output queue size 4
progress 40% @chr7:58000001, elapsed 0.8s, est remaining 1.2s, peak mem 1739MB, user 1.9s, sys 22.4s, output queue size 12
progress 45% @chr8:28000001, elapsed 0.9s, est remaining 1.1s, peak mem 1880MB, user 2.2s, sys 25.3s, output queue size 29
progress 50% @chr9:68000001, elapsed 1.0s, est remaining 1.0s, peak mem 1943MB, user 2.4s, sys 28.2s, output queue size 15
progress 55% @chr10:99000001, elapsed 1.1s, est remaining 0.9s, peak mem 2025MB, user 2.7s, sys 31.1s, output queue size 10
progress 60% @chr11:115000001, elapsed 1.2s, est remaining 0.8s, peak mem 2099MB, user 2.9s, sys 34.2s, output queue size 20
progress 65% @chr13:5000001, elapsed 1.3s, est remaining 0.7s, peak mem 2165MB, user 3.1s, sys 37.2s, output queue size 10
progress 70% @chr14:48000001, elapsed 1.4s, est remaining 0.6s, peak mem 2225MB, user 3.3s, sys 40.2s, output queue size 13
progress 75% @chr15:99000001, elapsed 1.5s, est remaining 0.5s, peak mem 2253MB, user 3.6s, sys 43.1s, output queue size 18
progress 80% @chr18:1, elapsed 1.6s, est remaining 0.4s, peak mem 2273MB, user 3.8s, sys 46.0s, output queue size 16
progress 85% @chr20:7000001, elapsed 1.7s, est remaining 0.3s, peak mem 2318MB, user 4.1s, sys 48.8s, output queue size 22
progress 90% @chrX:45000001, elapsed 2.1s, est remaining 0.2s, peak mem 2783MB, user 7.8s, sys 50.0s, output queue size 114
progress 95% @chrY:37000001, elapsed 2.3s, est remaining 0.1s, peak mem 2798MB, user 10.2s, sys 50.5s, output queue size 276
progress 100% @chr21:41000001, elapsed 5.6s, est remaining 0.0s, peak mem 2820MB, user 27.8s, sys 51.4s, 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: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 50044649
output file size: 93085578
reads: 1001838
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.021 real
ReadQualCal::delayed_init: 1 calls 0.001 user 0.000 sys 0.027 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 1.754 user 6.359 sys 7.894 real
done: 1 calls 0.328 user 0.538 sys 0.866 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.000 sys 5.671 real
fetch: 3219323 calls 0.192 user 6.261 sys 6.498 real
fetch_reads: 3219322 calls 0.346 user 6.048 sys 6.611 real
fetch_ref: 13004 calls 0.071 user 0.002 sys 0.053 real
fetch_vcf: 13004 calls 1.421 user 0.091 sys 1.628 real
idle: 2344 calls 2.725 user 0.395 sys 146.313 real
init: 1 calls 0.004 user 0.000 sys 0.033 real
update: 13229 calls 7.449 user 1.102 sys 9.363 real
write: 3219323 calls 12.250 user 5.826 sys 18.567 real
overall: 2957811712 mem 35.462 user 52.736 sys 7.930 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before Sig_18_tissue.table --after Sig_18_tissue.table.post Sig_18_tissue.csv
This software is licensed to bgold@natera.com by Sentieon Inc.
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: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.026 user 0.003 sys 0.028 real
done: 1 calls 0.054 user 0.005 sys 0.059 real
idle: 61 calls 0.002 user 0.000 sys 31.328 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 83640320 mem 0.071 user 0.040 sys 1.056 real