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/63/0784644c69dd1456906be74ac4e98f/1136_81F-T1-TDNA-1_A23MHWWLT4_1.table
  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-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/d7/1b324139cca8296b869f218bf8a14c/.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/e8/3e3d39f0664f31d4db697ffa24661d/1136_81F-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/1b324139cca8296b869f218bf8a14c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/3e3d39f0664f31d4db697ffa24661d/1136_81F-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  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_81F-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=1136_81F-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_81F-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 1136_81F-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 28.2s, est remaining 535.2s, peak mem 5470MB, user 703.5s, sys 7.8s, output queue size 52
progress 10% @chr2:81000001, elapsed 46.6s, est remaining 419.8s, peak mem 6600MB, user 1333.6s, sys 11.4s, output queue size 48
progress 15% @chr3:5000001, elapsed 67.0s, est remaining 379.9s, peak mem 7039MB, user 1935.9s, sys 15.0s, output queue size 122
progress 20% @chr3:168000001, elapsed 88.7s, est remaining 354.7s, peak mem 7103MB, user 2576.0s, sys 18.2s, output queue size 141
progress 25% @chr4:121000001, elapsed 107.8s, est remaining 323.3s, peak mem 7297MB, user 3151.4s, sys 21.8s, output queue size 114
progress 30% @chr5:1000001, elapsed 122.0s, est remaining 284.6s, peak mem 7315MB, user 3626.6s, sys 24.3s, output queue size 201
progress 35% @chr6:72000001, elapsed 144.2s, est remaining 267.7s, peak mem 7461MB, user 4214.3s, sys 27.5s, output queue size 106
progress 40% @chr7:67000001, elapsed 164.1s, est remaining 246.1s, peak mem 7678MB, user 4839.6s, sys 30.7s, output queue size 195
progress 45% @chr8:69000001, elapsed 188.4s, est remaining 230.3s, peak mem 7751MB, user 5573.6s, sys 34.3s, output queue size 117
progress 50% @chr9:88000001, elapsed 205.9s, est remaining 205.9s, peak mem 8013MB, user 6088.5s, sys 36.7s, output queue size 187
progress 55% @chr10:100000001, elapsed 229.6s, est remaining 187.8s, peak mem 8391MB, user 6841.7s, sys 41.3s, output queue size 150
progress 60% @chr11:134000001, elapsed 257.5s, est remaining 171.6s, peak mem 8701MB, user 7615.1s, sys 45.1s, output queue size 59
progress 65% @chr13:33000001, elapsed 280.6s, est remaining 151.1s, peak mem 8704MB, user 8297.0s, sys 49.0s, output queue size 209
progress 70% @chr14:78000001, elapsed 295.0s, est remaining 126.4s, peak mem 8879MB, user 8787.9s, sys 51.5s, output queue size 369
progress 75% @chr16:42000001, elapsed 319.5s, est remaining 106.5s, peak mem 8879MB, user 9528.7s, sys 54.7s, output queue size 118
progress 80% @chr18:1, elapsed 355.6s, est remaining 88.9s, peak mem 9012MB, user 10531.5s, sys 58.6s, output queue size 189
progress 85% @chr19:47000001, elapsed 389.4s, est remaining 68.7s, peak mem 9046MB, user 11615.8s, sys 63.2s, output queue size 80
progress 90% @chrX:35000001, elapsed 410.6s, est remaining 45.6s, peak mem 9046MB, user 12322.6s, sys 66.1s, output queue size 78
progress 95% @chrY:54000001, elapsed 428.1s, est remaining 22.5s, peak mem 9046MB, user 12851.5s, sys 68.4s, output queue size 211
progress 100% @chrX:154000001, elapsed 444.7s, est remaining 0.0s, peak mem 9046MB, user 13180.1s, sys 70.2s, output queue size 3453
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: 63239640700
output file size: 88646432873
reads: 1187143287
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.024 real
ReadQualCal::delayed_init: 1 calls 0.000 user 0.000 sys 0.038 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 1353.285 user 19.328 sys 1437.245 real
done: 1 calls 0.521 user 0.333 sys 0.854 real
exec_no_coor: 1 calls 0.129 user 0.039 sys 0.178 real
execute: 1 calls 0.005 user 0.000 sys 444.941 real
fetch: 3219323 calls 71.991 user 0.449 sys 105.953 real
fetch_reads: 3219322 calls 250.957 user 0.980 sys 261.250 real
fetch_ref: 2017177 calls 6.622 user 1.395 sys 8.456 real
fetch_vcf: 2017177 calls 102.798 user 1.886 sys 107.770 real
idle: 22270 calls 7.335 user 0.163 sys 363.263 real
init: 1 calls 0.003 user 0.000 sys 0.044 real
update: 2280904 calls 3072.198 user 4.890 sys 3235.595 real
write: 3219323 calls 9243.802 user 36.972 sys 9339.194 real
overall: 9485561856 mem 13196.346 user 96.154 sys 447.324 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1136_81F-T1-TDNA-1_A23MHWWLT4_1.table --after 1136_81F-T1-TDNA-1_A23MHWWLT4_1.table.post 1136_81F-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 0.049 user 0.001 sys 0.041 real
done: 1 calls 0.079 user 0.001 sys 0.078 real
idle: 61 calls 0.002 user 0.000 sys 31.311 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86777856 mem 0.113 user 0.014 sys 1.054 real