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/2a/38e78bb6942973beef9161c635e45e/1136_5Q-T1-TDNA-1_A23MHWWLT4_1.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/2a/38e78bb6942973beef9161c635e45e/1136_5Q-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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/32/012675d16572ae93df5a447e445194/1136_5Q-T1-TDNA-1_A23MHWWLT4_1.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/3ecc7da83db78e0b599a26f172db69/.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/cf/3ecc7da83db78e0b599a26f172db69/.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 1136_5Q-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=1136_5Q-T1-TDNA-1_A23MHWWLT4_1.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 1136_5Q-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 1136_5Q-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:153000001, elapsed 33.9s, est remaining 643.7s, peak mem 6021MB, user 841.9s, sys 9.3s, output queue size 44
progress 10% @chr2:90000001, elapsed 59.8s, est remaining 538.4s, peak mem 8348MB, user 1648.2s, sys 13.2s, output queue size 74
progress 15% @chr2:227000001, elapsed 87.6s, est remaining 496.4s, peak mem 9155MB, user 2461.0s, sys 16.5s, output queue size 203
progress 20% @chr3:176000001, elapsed 117.3s, est remaining 469.4s, peak mem 9319MB, user 3343.1s, sys 20.8s, output queue size 141
progress 25% @chr4:124000001, elapsed 142.8s, est remaining 428.3s, peak mem 9806MB, user 4126.9s, sys 23.9s, output queue size 302
progress 30% @chr5:101000001, elapsed 159.2s, est remaining 371.5s, peak mem 10004MB, user 4733.2s, sys 26.4s, output queue size 172
progress 35% @chr6:81000001, elapsed 183.5s, est remaining 340.7s, peak mem 10004MB, user 5410.1s, sys 29.6s, output queue size 106
progress 40% @chr7:56000001, elapsed 209.2s, est remaining 313.8s, peak mem 10582MB, user 6134.7s, sys 32.3s, output queue size 195
progress 45% @chr8:72000001, elapsed 239.7s, est remaining 292.9s, peak mem 10822MB, user 6969.0s, sys 35.7s, output queue size 356
progress 50% @chr9:89000001, elapsed 271.7s, est remaining 271.7s, peak mem 11280MB, user 7967.1s, sys 39.5s, output queue size 187
progress 55% @chr10:96000001, elapsed 300.3s, est remaining 245.7s, peak mem 11908MB, user 8855.6s, sys 43.0s, output queue size 348
progress 60% @chr11:126000001, elapsed 329.6s, est remaining 219.8s, peak mem 11908MB, user 9726.1s, sys 46.0s, output queue size 504
progress 65% @chr13:23000001, elapsed 357.1s, est remaining 192.3s, peak mem 11976MB, user 10572.7s, sys 49.4s, output queue size 474
progress 70% @chr13:28000001, elapsed 374.0s, est remaining 160.3s, peak mem 11976MB, user 11049.0s, sys 51.4s, output queue size 635
progress 75% @chr16:42000001, elapsed 405.8s, est remaining 135.3s, peak mem 11976MB, user 11845.1s, sys 54.2s, output queue size 797
progress 80% @chr18:29000001, elapsed 447.2s, est remaining 111.8s, peak mem 11976MB, user 13151.4s, sys 58.7s, output queue size 623
progress 85% @chr20:20000001, elapsed 489.6s, est remaining 86.4s, peak mem 11976MB, user 14622.3s, sys 63.5s, output queue size 351
progress 90% @chrX:30000001, elapsed 514.0s, est remaining 57.1s, peak mem 11976MB, user 15324.8s, sys 65.9s, output queue size 513
progress 95% @chrY:20000001, elapsed 529.3s, est remaining 27.9s, peak mem 11986MB, user 15748.9s, sys 67.6s, output queue size 675
progress 100% @chr22:23000001, elapsed 559.6s, est remaining 0.0s, peak mem 11986MB, user 16383.0s, sys 70.1s, output queue size 3635
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: 62212255172
output file size: 96036636036
reads: 1210780814
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.003 sys 0.016 real
ReadQualCal::delayed_init: 1 calls 0.008 user 0.002 sys 0.023 real
ReadQualCal::init: 1 calls 0.008 user 0.002 sys 0.006 real
advance: 3219322 calls 1379.535 user 19.952 sys 1431.861 real
done: 1 calls 0.548 user 0.260 sys 0.817 real
exec_no_coor: 1 calls 5.537 user 0.169 sys 5.725 real
execute: 1 calls 0.006 user 0.002 sys 560.522 real
fetch: 3219327 calls 73.815 user 0.342 sys 104.685 real
fetch_reads: 3219322 calls 273.364 user 1.046 sys 277.921 real
fetch_ref: 1998982 calls 7.258 user 1.574 sys 8.806 real
fetch_vcf: 1998982 calls 98.255 user 1.651 sys 104.928 real
idle: 41357 calls 21.592 user 0.229 sys 701.286 real
init: 1 calls 0.008 user 0.002 sys 0.029 real
update: 2350361 calls 3689.726 user 3.493 sys 3842.729 real
write: 3219327 calls 12390.723 user 37.202 sys 12543.693 real
overall: 12568502272 mem 16421.107 user 98.506 sys 562.939 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1136_5Q-T1-TDNA-1_A23MHWWLT4_1.table --after 1136_5Q-T1-TDNA-1_A23MHWWLT4_1.table.post 1136_5Q-T1-TDNA-1_A23MHWWLT4_1.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 0.042 user 0.008 sys 0.043 real
done: 1 calls 0.062 user 0.018 sys 0.080 real
idle: 61 calls 0.002 user 0.000 sys 31.319 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86806528 mem 0.080 user 0.050 sys 1.054 real