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/35/e5ec2619207d5c29b1df5ba5ea9ad2/1029_BCAN-N1-BDNA-1_B23KGCJLT4_1.table
  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-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/2f/18f3bc88f11b263aa6d4d43bcc1919/.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/52/d318c4d9427c5aeec440095e74c234/1029_BCAN-N1-BDNA-1_B23KGCJLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/d318c4d9427c5aeec440095e74c234/1029_BCAN-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/18f3bc88f11b263aa6d4d43bcc1919/.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 1029_BCAN-N1-BDNA-1_B23KGCJLT4_1.md.bam --read_filter QualCalFilter,table=1029_BCAN-N1-BDNA-1_B23KGCJLT4_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 1029_BCAN-N1-BDNA-1_B23KGCJLT4_1.table.post --algo ReadWriter 1029_BCAN-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:184000001, elapsed 9.5s, est remaining 180.9s, peak mem 3523MB, user 224.0s, sys 5.2s, output queue size 145
progress 10% @chr2:46000001, elapsed 16.8s, est remaining 151.3s, peak mem 3999MB, user 470.9s, sys 7.1s, output queue size 48
progress 15% @chr2:201000001, elapsed 25.2s, est remaining 143.1s, peak mem 4184MB, user 707.5s, sys 9.6s, output queue size 122
progress 20% @chr3:72000001, elapsed 32.3s, est remaining 129.2s, peak mem 4207MB, user 935.9s, sys 10.9s, output queue size 141
progress 25% @chr3:186000001, elapsed 38.8s, est remaining 116.4s, peak mem 4207MB, user 1131.9s, sys 12.0s, output queue size 302
progress 30% @chr5:107000001, elapsed 43.9s, est remaining 102.5s, peak mem 4207MB, user 1283.7s, sys 13.0s, output queue size 464
progress 35% @chr6:79000001, elapsed 51.0s, est remaining 94.7s, peak mem 4244MB, user 1469.2s, sys 14.2s, output queue size 625
progress 40% @chr7:65000001, elapsed 59.0s, est remaining 88.4s, peak mem 4333MB, user 1720.9s, sys 15.4s, output queue size 195
progress 45% @chr8:82000001, elapsed 67.6s, est remaining 82.6s, peak mem 4362MB, user 1984.9s, sys 16.7s, output queue size 204
progress 50% @chr9:88000001, elapsed 74.6s, est remaining 74.6s, peak mem 4409MB, user 2183.9s, sys 17.6s, output queue size 366
progress 55% @chr10:115000001, elapsed 83.1s, est remaining 68.0s, peak mem 4444MB, user 2442.4s, sys 18.6s, output queue size 348
progress 60% @chr11:134000001, elapsed 92.1s, est remaining 61.4s, peak mem 4444MB, user 2701.7s, sys 20.3s, output queue size 510
progress 65% @chr13:18000001, elapsed 100.7s, est remaining 54.2s, peak mem 4452MB, user 2947.9s, sys 21.7s, output queue size 672
progress 70% @chr13:102000001, elapsed 105.9s, est remaining 45.4s, peak mem 4461MB, user 3118.0s, sys 22.7s, output queue size 833
progress 75% @chr16:41000001, elapsed 115.1s, est remaining 38.4s, peak mem 4465MB, user 3409.5s, sys 24.5s, output queue size 461
progress 80% @chr17:50000001, elapsed 128.9s, est remaining 32.2s, peak mem 4484MB, user 3797.8s, sys 26.4s, output queue size 190
progress 85% @chr19:49000001, elapsed 140.7s, est remaining 24.8s, peak mem 4484MB, user 4193.4s, sys 27.9s, output queue size 351
progress 90% @chrX:36000001, elapsed 148.1s, est remaining 16.5s, peak mem 4529MB, user 4413.4s, sys 29.2s, output queue size 513
progress 95% @chrY:53000001, elapsed 152.4s, est remaining 8.0s, peak mem 4547MB, user 4536.8s, sys 29.8s, output queue size 675
progress 100% @chr22:23000001, elapsed 162.1s, est remaining 0.0s, peak mem 4547MB, user 4711.5s, sys 30.7s, 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: 13370650856
output file size: 22794885587
reads: 272165720
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.004 user 0.007 sys 0.023 real
ReadQualCal::delayed_init: 1 calls 0.006 user 0.001 sys 0.026 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 313.283 user 6.157 sys 328.401 real
done: 1 calls 0.493 user 0.704 sys 1.200 real
exec_no_coor: 1 calls 0.006 user 0.001 sys 0.007 real
execute: 1 calls 0.007 user 0.001 sys 162.444 real
fetch: 3219323 calls 12.356 user 0.396 sys 18.205 real
fetch_reads: 3219322 calls 57.269 user 0.679 sys 58.212 real
fetch_ref: 1388993 calls 4.790 user 1.083 sys 5.646 real
fetch_vcf: 1388993 calls 102.566 user 1.668 sys 105.087 real
idle: 8227 calls 5.049 user 0.081 sys 290.460 real
init: 1 calls 0.006 user 0.001 sys 0.032 real
update: 1465345 calls 1136.166 user 4.335 sys 1172.755 real
write: 3219323 calls 3344.355 user 12.929 sys 3375.066 real
overall: 4768391168 mem 4726.025 user 38.687 sys 165.034 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1029_BCAN-N1-BDNA-1_B23KGCJLT4_1.table --after 1029_BCAN-N1-BDNA-1_B23KGCJLT4_1.table.post 1029_BCAN-N1-BDNA-1_B23KGCJLT4_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 0.038 user 0.002 sys 0.043 real
done: 1 calls 0.069 user 0.011 sys 0.080 real
idle: 61 calls 0.002 user 0.000 sys 31.292 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86790144 mem 0.091 user 0.040 sys 1.055 real