Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/3498bfd2fcb7d554d2a6dd07e822e1/659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  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-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/b6/3498bfd2fcb7d554d2a6dd07e822e1/659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/246d82c1e7a45dde40a0b1bed0b234/.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-rnd-pltf-dev-nextflow-scratch-01/work/7b/1fda05ba75bf4c9b62babbaa90c07c/659_d0M-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.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/246d82c1e7a45dde40a0b1bed0b234/.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 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=659_d0M-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 659_d0M-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 659_d0M-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:153000001, elapsed 31.6s, est remaining 600.6s, peak mem 6259MB, user 811.8s, sys 8.2s, output queue size 42
progress 10% @chr2:46000001, elapsed 57.8s, est remaining 520.1s, peak mem 8580MB, user 1606.2s, sys 11.8s, output queue size 48
progress 15% @chr2:214000001, elapsed 90.7s, est remaining 513.8s, peak mem 10472MB, user 2505.1s, sys 15.0s, output queue size 203
progress 20% @chr3:161000001, elapsed 114.1s, est remaining 456.3s, peak mem 10559MB, user 3314.9s, sys 19.5s, output queue size 141
progress 25% @chr3:186000001, elapsed 136.1s, est remaining 408.3s, peak mem 10559MB, user 3990.7s, sys 22.1s, output queue size 302
progress 30% @chr5:81000001, elapsed 153.0s, est remaining 357.0s, peak mem 10612MB, user 4502.8s, sys 24.0s, output queue size 464
progress 35% @chr6:91000001, elapsed 177.4s, est remaining 329.5s, peak mem 10652MB, user 5135.9s, sys 26.1s, output queue size 625
progress 40% @chr7:65000001, elapsed 206.2s, est remaining 309.3s, peak mem 10962MB, user 5885.9s, sys 28.5s, output queue size 786
progress 45% @chr8:72000001, elapsed 238.9s, est remaining 291.9s, peak mem 11275MB, user 6989.4s, sys 32.1s, output queue size 204
progress 50% @chr9:76000001, elapsed 275.2s, est remaining 275.2s, peak mem 11960MB, user 7935.1s, sys 35.3s, output queue size 366
progress 55% @chr10:101000001, elapsed 317.1s, est remaining 259.4s, peak mem 12098MB, user 9112.2s, sys 38.6s, output queue size 527
progress 60% @chr11:134000001, elapsed 359.2s, est remaining 239.5s, peak mem 12098MB, user 10473.5s, sys 42.3s, output queue size 510
progress 65% @chr13:33000001, elapsed 401.4s, est remaining 216.2s, peak mem 12139MB, user 11598.5s, sys 45.0s, output queue size 672
progress 70% @chr14:71000001, elapsed 425.4s, est remaining 182.3s, peak mem 12139MB, user 12471.7s, sys 47.4s, output queue size 833
progress 75% @chr16:42000001, elapsed 467.1s, est remaining 155.7s, peak mem 12270MB, user 13779.6s, sys 50.8s, output queue size 461
progress 80% @chr18:25000001, elapsed 518.3s, est remaining 129.6s, peak mem 12270MB, user 15163.1s, sys 54.3s, output queue size 623
progress 85% @chr20:18000001, elapsed 565.1s, est remaining 99.7s, peak mem 12270MB, user 16689.9s, sys 57.9s, output queue size 785
progress 90% @chrX:32000001, elapsed 597.4s, est remaining 66.4s, peak mem 12388MB, user 17823.5s, sys 61.3s, output queue size 513
progress 95% @chrY:54000001, elapsed 619.7s, est remaining 32.6s, peak mem 12388MB, user 18555.3s, sys 63.5s, output queue size 239
progress 100% @chrX:67000001, elapsed 654.0s, est remaining 0.0s, peak mem 12388MB, user 19250.0s, sys 65.7s, output queue size 3540
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: 62651370106
output file size: 96298931986
reads: 1242257820
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.014 real
ReadQualCal::delayed_init: 1 calls 0.007 user 0.003 sys 0.025 real
ReadQualCal::init: 1 calls 0.001 user 0.009 sys 0.006 real
advance: 3219322 calls 1637.962 user 22.560 sys 1684.130 real
done: 1 calls 0.509 user 0.419 sys 0.930 real
exec_no_coor: 1 calls 0.000 user 0.022 sys 0.036 real
execute: 1 calls 0.000 user 0.001 sys 654.692 real
fetch: 3219323 calls 93.440 user 0.518 sys 132.532 real
fetch_reads: 3219322 calls 304.674 user 1.259 sys 307.298 real
fetch_ref: 1883061 calls 6.989 user 1.278 sys 8.414 real
fetch_vcf: 1883061 calls 110.908 user 1.684 sys 115.619 real
idle: 33431 calls 18.803 user 0.193 sys 696.231 real
init: 1 calls 0.007 user 0.009 sys 0.031 real
update: 2193458 calls 4086.133 user 2.837 sys 4189.780 real
write: 3219323 calls 14650.615 user 30.974 sys 14812.017 real
overall: 12990394368 mem 19283.756 user 96.606 sys 657.250 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 659_d0M-T1-TDNA-1_A23MHWWLT4_1.table --after 659_d0M-T1-TDNA-1_A23MHWWLT4_1.table.post 659_d0M-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 0.039 user 0.001 sys 0.040 real
done: 1 calls 0.079 user 0.001 sys 0.077 real
idle: 61 calls 0.002 user 0.000 sys 31.388 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86794240 mem 0.107 user 0.021 sys 1.062 real