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/65/17f667fb2215f6b86c9d6a671dfad5/Sig_18_Blood.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/8eee459d74eba64dfe5bc8368d5cb4/.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/e4/8eee459d74eba64dfe5bc8368d5cb4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/bbf3839dfd2c68f28e02f3d64e69ad/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/bbf3839dfd2c68f28e02f3d64e69ad/Sig_18_Blood.md.bam.bai
  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 Sig_18_Blood.md.bam --read_filter QualCalFilter,table=Sig_18_Blood.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 Sig_18_Blood.table.post --algo ReadWriter Sig_18_Blood.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:179000001, elapsed 0.3s, est remaining 6.1s, peak mem 295MB, user 0.5s, sys 8.0s, output queue size 25
progress 10% @chr2:61000001, elapsed 0.6s, est remaining 5.4s, peak mem 460MB, user 0.9s, sys 16.3s, output queue size 41
progress 15% @chr2:222000001, elapsed 0.9s, est remaining 4.9s, peak mem 562MB, user 1.3s, sys 24.3s, output queue size 19
progress 20% @chr3:175000001, elapsed 1.1s, est remaining 4.5s, peak mem 676MB, user 1.7s, sys 31.8s, output queue size 23
progress 25% @chr4:110000001, elapsed 1.4s, est remaining 4.2s, peak mem 757MB, user 2.1s, sys 39.9s, output queue size 17
progress 30% @chr5:102000001, elapsed 1.7s, est remaining 3.9s, peak mem 805MB, user 2.5s, sys 47.7s, output queue size 8
progress 35% @chr6:75000001, elapsed 1.9s, est remaining 3.6s, peak mem 868MB, user 2.7s, sys 55.7s, output queue size 8
progress 40% @chr7:59000001, elapsed 2.2s, est remaining 3.3s, peak mem 925MB, user 3.0s, sys 63.3s, output queue size 17
progress 45% @chr8:44000001, elapsed 2.4s, est remaining 3.0s, peak mem 994MB, user 3.4s, sys 70.6s, output queue size 65
progress 50% @chr9:59000001, elapsed 2.7s, est remaining 2.7s, peak mem 1090MB, user 3.8s, sys 78.4s, output queue size 14
progress 55% @chr10:99000001, elapsed 3.0s, est remaining 2.4s, peak mem 1162MB, user 4.3s, sys 86.1s, output queue size 16
progress 60% @chr11:103000001, elapsed 3.2s, est remaining 2.2s, peak mem 1237MB, user 4.7s, sys 93.9s, output queue size 33
progress 65% @chr13:27000001, elapsed 3.5s, est remaining 1.9s, peak mem 1306MB, user 5.2s, sys 101.8s, output queue size 23
progress 70% @chr14:68000001, elapsed 3.8s, est remaining 1.6s, peak mem 1408MB, user 5.7s, sys 109.5s, output queue size 13
progress 75% @chr16:20000001, elapsed 4.0s, est remaining 1.3s, peak mem 1444MB, user 6.0s, sys 116.9s, output queue size 17
progress 80% @chr18:5000001, elapsed 4.3s, est remaining 1.1s, peak mem 1507MB, user 6.5s, sys 125.0s, output queue size 10
progress 85% @chr20:28000001, elapsed 4.6s, est remaining 0.8s, peak mem 1573MB, user 6.9s, sys 132.9s, output queue size 12
progress 90% @chrX:44000001, elapsed 5.1s, est remaining 0.6s, peak mem 2686MB, user 11.4s, sys 137.7s, output queue size 114
progress 95% @chrY:44000001, elapsed 5.3s, est remaining 0.3s, peak mem 2704MB, user 14.6s, sys 141.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 7.2s, est remaining 0.0s, peak mem 2710MB, user 27.0s, sys 146.5s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 52290603
output file size: 74586809
reads: 1001133
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.030 real
ReadQualCal::delayed_init: 1 calls 0.005 user 0.001 sys 0.023 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 1.751 user 18.684 sys 20.477 real
done: 1 calls 0.454 user 0.772 sys 1.235 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.000 sys 7.333 real
fetch: 3219322 calls 0.361 user 18.743 sys 15.732 real
fetch_reads: 3219322 calls 0.544 user 17.381 sys 15.980 real
fetch_ref: 13318 calls 0.051 user 0.039 sys 0.083 real
fetch_vcf: 13318 calls 1.370 user 0.140 sys 1.570 real
idle: 1534 calls 1.254 user 0.336 sys 108.076 real
init: 1 calls 0.007 user 0.001 sys 0.029 real
update: 13537 calls 7.819 user 2.456 sys 11.113 real
write: 3219322 calls 9.706 user 19.459 sys 28.215 real
overall: 2842640384 mem 31.367 user 148.424 sys 9.680 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before Sig_18_Blood.table --after Sig_18_Blood.table.post Sig_18_Blood.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: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.030 user 0.000 sys 0.029 real
done: 1 calls 0.060 user 0.000 sys 0.063 real
idle: 61 calls 0.002 user 0.000 sys 31.352 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81854464 mem 0.077 user 0.044 sys 1.056 real