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/b1/80c7a3c2df156fb3104ea9d1721b43/1029_FZX-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-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/f2/e6b4191e428c9047c9d238d62bd917/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/1a7d4d315d77678c4e8d70aef1fcfc/.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/b1/80c7a3c2df156fb3104ea9d1721b43/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/1a7d4d315d77678c4e8d70aef1fcfc/.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_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=1029_FZX-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 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:169000001, elapsed 31.3s, est remaining 594.5s, peak mem 5767MB, user 744.2s, sys 6.7s, output queue size 145
progress 10% @chr2:58000001, elapsed 57.7s, est remaining 519.5s, peak mem 9195MB, user 1587.6s, sys 10.9s, output queue size 48
progress 15% @chr2:211000001, elapsed 91.9s, est remaining 520.5s, peak mem 10358MB, user 2581.7s, sys 15.3s, output queue size 203
progress 20% @chr3:174000001, elapsed 120.8s, est remaining 483.1s, peak mem 10678MB, user 3495.9s, sys 20.5s, output queue size 141
progress 25% @chr4:135000001, elapsed 141.5s, est remaining 424.4s, peak mem 10678MB, user 4134.6s, sys 22.8s, output queue size 302
progress 30% @chr5:104000001, elapsed 158.6s, est remaining 370.0s, peak mem 10743MB, user 4681.5s, sys 24.7s, output queue size 464
progress 35% @chr6:56000001, elapsed 185.8s, est remaining 345.1s, peak mem 10993MB, user 5349.0s, sys 27.3s, output queue size 625
progress 40% @chr7:67000001, elapsed 214.3s, est remaining 321.5s, peak mem 11298MB, user 6257.2s, sys 30.4s, output queue size 195
progress 45% @chr8:77000001, elapsed 248.0s, est remaining 303.1s, peak mem 11648MB, user 7265.7s, sys 33.8s, output queue size 204
progress 50% @chr9:88000001, elapsed 275.6s, est remaining 275.6s, peak mem 12080MB, user 8032.1s, sys 36.9s, output queue size 324
progress 55% @chr10:118000001, elapsed 307.0s, est remaining 251.2s, peak mem 12569MB, user 8999.7s, sys 40.4s, output queue size 348
progress 60% @chr11:117000001, elapsed 337.2s, est remaining 224.8s, peak mem 12569MB, user 9934.7s, sys 43.6s, output queue size 510
progress 65% @chr13:33000001, elapsed 370.7s, est remaining 199.6s, peak mem 12770MB, user 10921.9s, sys 46.7s, output queue size 474
progress 70% @chr14:79000001, elapsed 390.8s, est remaining 167.5s, peak mem 12770MB, user 11639.9s, sys 49.0s, output queue size 299
progress 75% @chr16:42000001, elapsed 427.3s, est remaining 142.4s, peak mem 12770MB, user 12569.2s, sys 52.0s, output queue size 461
progress 80% @chr18:25000001, elapsed 491.6s, est remaining 122.9s, peak mem 12787MB, user 14196.1s, sys 56.5s, output queue size 623
progress 85% @chr19:15000001, elapsed 547.0s, est remaining 96.5s, peak mem 12787MB, user 16254.6s, sys 62.3s, output queue size 351
progress 90% @chrX:20000001, elapsed 587.2s, est remaining 65.2s, peak mem 13005MB, user 17434.0s, sys 65.6s, output queue size 513
progress 95% @chrY:55000001, elapsed 607.5s, est remaining 32.0s, peak mem 13005MB, user 18183.4s, sys 67.8s, output queue size 240
progress 100% @chr22:23000001, elapsed 642.1s, est remaining 0.0s, peak mem 13005MB, user 18856.8s, sys 69.8s, output queue size 3635
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 67770633046
output file size: 102263490723
reads: 1275212856
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.011 real
ReadQualCal::delayed_init: 1 calls 0.004 user 0.002 sys 0.021 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 1641.330 user 24.061 sys 1695.902 real
done: 1 calls 0.504 user 0.407 sys 0.915 real
exec_no_coor: 1 calls 0.005 user 0.010 sys 0.026 real
execute: 1 calls 0.004 user 0.000 sys 643.665 real
fetch: 3219323 calls 96.969 user 0.455 sys 138.740 real
fetch_reads: 3219322 calls 320.607 user 1.279 sys 325.011 real
fetch_ref: 2031444 calls 7.404 user 1.467 sys 8.739 real
fetch_vcf: 2031444 calls 102.211 user 1.944 sys 106.132 real
idle: 34931 calls 28.775 user 0.236 sys 741.686 real
init: 1 calls 0.008 user 0.002 sys 0.027 real
update: 2358556 calls 4191.934 user 3.005 sys 4310.180 real
write: 3219323 calls 14267.288 user 33.210 sys 14415.355 real
overall: 13637632000 mem 18905.757 user 108.379 sys 646.323 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.table --after 1029_FZX-T1-TDNA-1_A23MHWWLT4_1.table.post 1029_FZX-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: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.020 user 0.010 sys 0.041 real
done: 1 calls 0.060 user 0.020 sys 0.079 real
idle: 60 calls 0.002 user 0.000 sys 31.386 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86794240 mem 0.097 user 0.032 sys 1.054 real