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/2b/326aaa2df46cc380a5d93690b336f5/.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/72/7ad39e35b02be6d8caa1b512c1dfc4/1029_HTI-T1-TDNA-1_A23MHWWLT4_1.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/326aaa2df46cc380a5d93690b336f5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/db10c5a483ab5aeea888c988e22091/1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/db10c5a483ab5aeea888c988e22091/1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=1029_HTI-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_HTI-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 32.3s, est remaining 614.4s, peak mem 5996MB, user 808.3s, sys 8.7s, output queue size 42
progress 10% @chr2:46000001, elapsed 58.7s, est remaining 527.9s, peak mem 7702MB, user 1618.6s, sys 12.3s, output queue size 48
progress 15% @chr2:230000001, elapsed 89.0s, est remaining 504.5s, peak mem 8518MB, user 2540.4s, sys 17.1s, output queue size 122
progress 20% @chr3:136000001, elapsed 114.1s, est remaining 456.5s, peak mem 8611MB, user 3313.0s, sys 20.0s, output queue size 141
progress 25% @chr4:136000001, elapsed 136.3s, est remaining 408.9s, peak mem 8845MB, user 3981.5s, sys 22.9s, output queue size 302
progress 30% @chr5:107000001, elapsed 155.0s, est remaining 361.6s, peak mem 8895MB, user 4571.2s, sys 25.1s, output queue size 464
progress 35% @chr6:44000001, elapsed 180.2s, est remaining 334.7s, peak mem 8943MB, user 5287.9s, sys 27.8s, output queue size 106
progress 40% @chr7:41000001, elapsed 207.2s, est remaining 310.8s, peak mem 9120MB, user 6101.7s, sys 31.0s, output queue size 195
progress 45% @chr8:72000001, elapsed 243.1s, est remaining 297.1s, peak mem 9644MB, user 7083.1s, sys 34.6s, output queue size 204
progress 50% @chr9:81000001, elapsed 269.6s, est remaining 269.6s, peak mem 9933MB, user 7876.1s, sys 37.5s, output queue size 324
progress 55% @chr10:115000001, elapsed 300.7s, est remaining 246.1s, peak mem 10068MB, user 8819.2s, sys 40.7s, output queue size 348
progress 60% @chr12:1000001, elapsed 334.4s, est remaining 222.9s, peak mem 10068MB, user 9812.4s, sys 44.1s, output queue size 510
progress 65% @chr13:23000001, elapsed 363.7s, est remaining 195.8s, peak mem 10223MB, user 10826.9s, sys 47.2s, output queue size 138
progress 70% @chr14:78000001, elapsed 384.1s, est remaining 164.6s, peak mem 10223MB, user 11430.9s, sys 49.1s, output queue size 299
progress 75% @chr16:42000001, elapsed 419.5s, est remaining 139.8s, peak mem 10330MB, user 12367.9s, sys 52.9s, output queue size 461
progress 80% @chr17:58000001, elapsed 465.6s, est remaining 116.4s, peak mem 10415MB, user 13775.8s, sys 57.1s, output queue size 190
progress 85% @chr19:49000001, elapsed 508.2s, est remaining 89.7s, peak mem 10415MB, user 15157.0s, sys 61.6s, output queue size 351
progress 90% @chrX:18000001, elapsed 541.3s, est remaining 60.1s, peak mem 10712MB, user 16100.9s, sys 64.5s, output queue size 513
progress 95% @chrY:52000001, elapsed 565.0s, est remaining 29.7s, peak mem 10712MB, user 16921.8s, sys 67.3s, output queue size 211
progress 100% @chrX:67000001, elapsed 595.2s, est remaining 0.0s, peak mem 10712MB, user 17498.5s, sys 69.3s, 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: 74334244054
output file size: 109009441980
reads: 1460016157
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.011 real
ReadQualCal::delayed_init: 1 calls 0.002 user 0.001 sys 0.025 real
ReadQualCal::init: 1 calls 0.001 user 0.009 sys 0.006 real
advance: 3219322 calls 1694.932 user 22.027 sys 1761.531 real
done: 1 calls 0.590 user 0.249 sys 0.845 real
exec_no_coor: 1 calls 0.122 user 0.061 sys 0.214 real
execute: 1 calls 0.005 user 0.000 sys 595.977 real
fetch: 3219323 calls 99.951 user 0.532 sys 147.372 real
fetch_reads: 3219322 calls 329.432 user 0.982 sys 337.106 real
fetch_ref: 2104998 calls 6.795 user 1.393 sys 8.377 real
fetch_vcf: 2104998 calls 95.306 user 1.555 sys 100.162 real
idle: 44461 calls 10.932 user 0.165 sys 643.772 real
init: 1 calls 0.004 user 0.001 sys 0.032 real
update: 2473231 calls 3884.233 user 3.107 sys 4022.172 real
write: 3219323 calls 12882.987 user 35.047 sys 13048.823 real
overall: 11232542720 mem 17521.433 user 103.165 sys 598.389 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.table --after 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.table.post 1029_HTI-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 0.037 user 0.003 sys 0.040 real
done: 1 calls 0.065 user 0.005 sys 0.079 real
idle: 61 calls 0.002 user 0.000 sys 31.376 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86810624 mem 0.100 user 0.030 sys 1.060 real