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/ab/115b64305d060833379ba5675af81f/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/55/a49026cb49cc8dd6ad31be4a0e0bdf/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/ab/115b64305d060833379ba5675af81f/Sig_18_tissue.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/a954511b40e76d107ffbd247f3a138/.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/79/a954511b40e76d107ffbd247f3a138/.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% @chr1:166000001, elapsed 0.1s, est remaining 2.2s, peak mem 401MB, user 0.3s, sys 2.7s, output queue size 6
progress 10% @chr2:64000001, elapsed 0.2s, est remaining 1.9s, peak mem 779MB, user 0.6s, sys 5.3s, output queue size 41
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.7s, peak mem 989MB, user 0.8s, sys 7.9s, output queue size 24
progress 20% @chr3:152000001, elapsed 0.4s, est remaining 1.6s, peak mem 1136MB, user 1.0s, sys 10.4s, output queue size 1
progress 25% @chr4:112000001, elapsed 0.5s, est remaining 1.5s, peak mem 1310MB, user 1.3s, sys 13.5s, output queue size 20
progress 30% @chr5:83000001, elapsed 0.7s, est remaining 1.6s, peak mem 1526MB, user 1.7s, sys 18.1s, output queue size 26
progress 35% @chr6:59000001, elapsed 0.8s, est remaining 1.5s, peak mem 1640MB, user 2.0s, sys 22.6s, output queue size 13
progress 40% @chr7:76000001, elapsed 1.1s, est remaining 1.6s, peak mem 1745MB, user 2.4s, sys 29.0s, output queue size 12
progress 45% @chr8:49000001, elapsed 1.3s, est remaining 1.6s, peak mem 1847MB, user 2.8s, sys 35.6s, output queue size 23
progress 50% @chr9:39000001, elapsed 1.5s, est remaining 1.5s, peak mem 1970MB, user 3.2s, sys 42.1s, output queue size 35
progress 55% @chr10:115000001, elapsed 1.7s, est remaining 1.4s, peak mem 2027MB, user 3.7s, sys 48.7s, output queue size 27
progress 60% @chr11:118000001, elapsed 2.0s, est remaining 1.3s, peak mem 2090MB, user 4.1s, sys 55.5s, output queue size 34
progress 65% @chr13:13000001, elapsed 2.2s, est remaining 1.2s, peak mem 2132MB, user 4.6s, sys 62.1s, output queue size 30
progress 70% @chr14:58000001, elapsed 2.4s, est remaining 1.0s, peak mem 2180MB, user 5.1s, sys 68.8s, output queue size 11
progress 75% @chr15:55000001, elapsed 2.7s, est remaining 0.9s, peak mem 2225MB, user 5.5s, sys 75.5s, output queue size 60
progress 80% @chr18:7000001, elapsed 2.9s, est remaining 0.7s, peak mem 2261MB, user 5.8s, sys 82.0s, output queue size 83
progress 85% @chr20:17000001, elapsed 3.1s, est remaining 0.5s, peak mem 2306MB, user 6.1s, sys 88.7s, output queue size 57
progress 90% @chrX:47000001, elapsed 3.5s, est remaining 0.4s, peak mem 2750MB, user 9.2s, sys 91.1s, output queue size 114
progress 95% @chrY:40000001, elapsed 3.7s, est remaining 0.2s, peak mem 2771MB, user 13.4s, sys 92.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 7.5s, est remaining 0.0s, peak mem 2786MB, user 30.8s, sys 95.5s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 50047057
output file size: 93248816
reads: 1001838
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.007 user 0.002 sys 0.014 real
ReadQualCal::delayed_init: 1 calls 0.004 user 0.000 sys 0.027 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 1.477 user 11.960 sys 13.582 real
done: 1 calls 0.339 user 0.477 sys 0.819 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.007 user 0.001 sys 7.597 real
fetch: 3219323 calls 0.214 user 11.536 sys 11.288 real
fetch_reads: 3219322 calls 0.319 user 12.028 sys 11.374 real
fetch_ref: 13004 calls 0.076 user 0.028 sys 0.056 real
fetch_vcf: 13004 calls 1.533 user 0.102 sys 1.620 real
idle: 1955 calls 1.554 user 0.303 sys 159.148 real
init: 1 calls 0.004 user 0.000 sys 0.033 real
update: 13229 calls 8.255 user 1.094 sys 9.773 real
write: 3219323 calls 13.272 user 12.441 sys 25.301 real
overall: 2922151936 mem 37.129 user 96.827 sys 9.796 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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.020 user 0.010 sys 0.028 real
done: 1 calls 0.039 user 0.020 sys 0.059 real
idle: 61 calls 0.002 user 0.000 sys 31.276 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81936384 mem 0.066 user 0.047 sys 1.052 real