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/94/8f486a46091712a9fa4e775bd800a1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/5fc9bb2de61c58baad3eeeb46f3e72/.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/8f/456c7297230f9d5b53e61a8b972390/1136_4GR-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.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/456c7297230f9d5b53e61a8b972390/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/5fc9bb2de61c58baad3eeeb46f3e72/.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_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=1136_4GR-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_4GR-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:178000001, elapsed 27.0s, est remaining 513.7s, peak mem 5372MB, user 640.3s, sys 6.8s, output queue size 145
progress 10% @chr2:90000001, elapsed 48.3s, est remaining 435.0s, peak mem 6999MB, user 1350.4s, sys 10.6s, output queue size 48
progress 15% @chr2:197000001, elapsed 71.7s, est remaining 406.3s, peak mem 7371MB, user 2046.9s, sys 13.9s, output queue size 122
progress 20% @chr3:129000001, elapsed 92.4s, est remaining 369.6s, peak mem 7371MB, user 2669.0s, sys 16.0s, output queue size 141
progress 25% @chr4:87000001, elapsed 109.3s, est remaining 327.9s, peak mem 7371MB, user 3185.6s, sys 17.9s, output queue size 302
progress 30% @chr5:104000001, elapsed 122.4s, est remaining 285.7s, peak mem 7374MB, user 3604.7s, sys 19.5s, output queue size 464
progress 35% @chr6:56000001, elapsed 143.5s, est remaining 266.5s, peak mem 7567MB, user 4185.6s, sys 21.9s, output queue size 106
progress 40% @chr7:45000001, elapsed 166.4s, est remaining 249.6s, peak mem 7892MB, user 4843.1s, sys 24.7s, output queue size 197
progress 45% @chr8:66000001, elapsed 191.3s, est remaining 233.9s, peak mem 8035MB, user 5574.3s, sys 27.9s, output queue size 204
progress 50% @chr9:21000001, elapsed 215.7s, est remaining 215.7s, peak mem 8266MB, user 6298.1s, sys 30.5s, output queue size 187
progress 55% @chr10:62000001, elapsed 243.5s, est remaining 199.2s, peak mem 8401MB, user 7180.3s, sys 33.1s, output queue size 348
progress 60% @chr11:134000001, elapsed 273.6s, est remaining 182.4s, peak mem 8469MB, user 8065.4s, sys 36.1s, output queue size 312
progress 65% @chr13:25000001, elapsed 299.7s, est remaining 161.4s, peak mem 8536MB, user 8915.2s, sys 38.7s, output queue size 138
progress 70% @chr14:35000001, elapsed 316.6s, est remaining 135.7s, peak mem 8563MB, user 9421.3s, sys 40.3s, output queue size 299
progress 75% @chr16:42000001, elapsed 342.5s, est remaining 114.2s, peak mem 8597MB, user 10138.8s, sys 43.5s, output queue size 461
progress 80% @chr18:11000001, elapsed 383.4s, est remaining 95.8s, peak mem 8667MB, user 11241.4s, sys 47.2s, output queue size 623
progress 85% @chr19:52000001, elapsed 418.6s, est remaining 73.9s, peak mem 8667MB, user 12443.5s, sys 50.8s, output queue size 351
progress 90% @chrX:20000001, elapsed 444.3s, est remaining 49.4s, peak mem 8789MB, user 13320.7s, sys 53.7s, output queue size 78
progress 95% @chrY:54000001, elapsed 458.0s, est remaining 24.1s, peak mem 8861MB, user 13715.1s, sys 55.4s, output queue size 240
progress 100% @chr22:23000001, elapsed 485.6s, est remaining 0.0s, peak mem 8861MB, user 14146.2s, sys 57.3s, 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: 54881652601
output file size: 82354231418
reads: 1048916945
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.014 real
ReadQualCal::delayed_init: 1 calls 0.002 user 0.001 sys 0.023 real
ReadQualCal::init: 1 calls 0.000 user 0.010 sys 0.006 real
advance: 3219322 calls 1265.763 user 18.517 sys 1310.325 real
done: 1 calls 0.580 user 0.279 sys 0.864 real
exec_no_coor: 1 calls 0.000 user 0.014 sys 0.045 real
execute: 1 calls 0.002 user 0.000 sys 486.499 real
fetch: 3219323 calls 68.429 user 0.447 sys 102.771 real
fetch_reads: 3219322 calls 240.893 user 0.802 sys 248.609 real
fetch_ref: 2044035 calls 6.385 user 1.484 sys 8.076 real
fetch_vcf: 2044035 calls 98.428 user 1.735 sys 102.895 real
idle: 23785 calls 5.816 user 0.098 sys 681.179 real
init: 1 calls 0.007 user 0.001 sys 0.029 real
update: 2331253 calls 3323.624 user 3.202 sys 3425.926 real
write: 3219323 calls 10366.841 user 26.674 sys 10510.275 real
overall: 9291636736 mem 14162.947 user 84.081 sys 488.988 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.table --after 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.table.post 1136_4GR-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 0.040 user 0.030 sys 0.078 real
idle: 61 calls 0.002 user 0.000 sys 31.313 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86712320 mem 0.066 user 0.066 sys 1.061 real