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/cd/7ac33d45a08167ab78c9b6a3578b74/1136_7OW-T1-TDNA-1_A23MHWWLT4_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-rnd-pltf-dev-nextflow-scratch-01/work/0a/17fccdf819f8ec4c552cea4ecfb06f/1136_7OW-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/0a/17fccdf819f8ec4c552cea4ecfb06f/1136_7OW-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/f2/3aaa77c394c6b4262ba3f6d3d4c0be/.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/f2/3aaa77c394c6b4262ba3f6d3d4c0be/.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_7OW-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=1136_7OW-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_7OW-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 36.5s, est remaining 693.7s, peak mem 6513MB, user 876.2s, sys 8.2s, output queue size 145
progress 10% @chr2:69000001, elapsed 63.9s, est remaining 575.2s, peak mem 8866MB, user 1803.7s, sys 12.1s, output queue size 48
progress 15% @chr2:237000001, elapsed 96.3s, est remaining 545.5s, peak mem 9669MB, user 2687.7s, sys 15.4s, output queue size 203
progress 20% @chr3:128000001, elapsed 123.2s, est remaining 492.8s, peak mem 9874MB, user 3583.5s, sys 19.4s, output queue size 141
progress 25% @chr4:83000001, elapsed 147.7s, est remaining 443.2s, peak mem 10126MB, user 4301.2s, sys 22.1s, output queue size 302
progress 30% @chr5:83000001, elapsed 167.5s, est remaining 390.8s, peak mem 10200MB, user 4890.3s, sys 24.2s, output queue size 464
progress 35% @chr6:79000001, elapsed 195.0s, est remaining 362.1s, peak mem 10350MB, user 5641.5s, sys 26.7s, output queue size 625
progress 40% @chr7:65000001, elapsed 225.8s, est remaining 338.6s, peak mem 11032MB, user 6511.1s, sys 29.9s, output queue size 197
progress 45% @chr8:72000001, elapsed 261.3s, est remaining 319.4s, peak mem 11385MB, user 7651.0s, sys 33.8s, output queue size 204
progress 50% @chr9:89000001, elapsed 287.9s, est remaining 287.9s, peak mem 11488MB, user 8393.7s, sys 36.6s, output queue size 366
progress 55% @chr10:118000001, elapsed 320.0s, est remaining 261.8s, peak mem 11545MB, user 9398.0s, sys 40.0s, output queue size 348
progress 60% @chr11:117000001, elapsed 353.9s, est remaining 235.9s, peak mem 11545MB, user 10410.0s, sys 43.4s, output queue size 510
progress 65% @chr13:19000001, elapsed 385.9s, est remaining 207.8s, peak mem 11545MB, user 11304.0s, sys 46.3s, output queue size 672
progress 70% @chr14:79000001, elapsed 406.3s, est remaining 174.1s, peak mem 11565MB, user 12186.0s, sys 48.9s, output queue size 299
progress 75% @chr16:42000001, elapsed 441.2s, est remaining 147.1s, peak mem 11565MB, user 13037.3s, sys 51.7s, output queue size 461
progress 80% @chr18:25000001, elapsed 492.7s, est remaining 123.2s, peak mem 11565MB, user 14414.5s, sys 55.8s, output queue size 623
progress 85% @chr20:20000001, elapsed 534.9s, est remaining 94.4s, peak mem 11589MB, user 15977.6s, sys 60.2s, output queue size 351
progress 90% @chrX:34000001, elapsed 563.0s, est remaining 62.6s, peak mem 11589MB, user 16808.9s, sys 62.7s, output queue size 513
progress 95% @chrY:55000001, elapsed 580.6s, est remaining 30.6s, peak mem 11625MB, user 17252.4s, sys 64.2s, output queue size 675
progress 100% @chr22:23000001, elapsed 612.4s, est remaining 0.0s, peak mem 11625MB, user 17939.7s, sys 66.6s, 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: 66871250911
output file size: 102256539585
reads: 1299975145
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.003 user 0.003 sys 0.014 real
ReadQualCal::delayed_init: 1 calls 0.005 user 0.001 sys 0.026 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 1515.333 user 22.003 sys 1568.346 real
done: 1 calls 0.514 user 0.391 sys 0.910 real
exec_no_coor: 1 calls 0.008 user 0.015 sys 0.040 real
execute: 1 calls 0.007 user 0.001 sys 613.426 real
fetch: 3219323 calls 90.694 user 0.509 sys 131.378 real
fetch_reads: 3219322 calls 301.761 user 0.819 sys 305.848 real
fetch_ref: 2084644 calls 7.033 user 1.327 sys 8.427 real
fetch_vcf: 2084644 calls 96.444 user 1.749 sys 100.335 real
idle: 31356 calls 9.195 user 0.172 sys 765.017 real
init: 1 calls 0.005 user 0.001 sys 0.032 real
update: 2440689 calls 3950.602 user 2.977 sys 4069.634 real
write: 3219323 calls 13639.600 user 32.624 sys 13803.270 real
overall: 12190326784 mem 17962.255 user 102.676 sys 616.090 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.table --after 1136_7OW-T1-TDNA-1_A23MHWWLT4_1.table.post 1136_7OW-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 0.036 user 0.008 sys 0.040 real
done: 1 calls 0.056 user 0.017 sys 0.079 real
idle: 60 calls 0.002 user 0.000 sys 31.291 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86810624 mem 0.082 user 0.051 sys 1.058 real