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/d2/49f12bcb454d653dd137afdbd7d4b6/Sig_18_Blood.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/b9327ccd07f95c93afdb2eed727086/.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/b8/09ab92fd6d06dd30552109cbffc247/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/b9327ccd07f95c93afdb2eed727086/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/09ab92fd6d06dd30552109cbffc247/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% @chr1:159000001, elapsed 0.2s, est remaining 3.5s, peak mem 287MB, user 0.3s, sys 4.3s, output queue size 13
progress 10% @chr2:57000001, elapsed 0.3s, est remaining 3.1s, peak mem 515MB, user 0.7s, sys 9.3s, output queue size 41
progress 15% @chr2:240000001, elapsed 0.5s, est remaining 2.6s, peak mem 614MB, user 1.1s, sys 12.3s, output queue size 18
progress 20% @chr3:156000001, elapsed 0.6s, est remaining 2.3s, peak mem 740MB, user 1.3s, sys 15.3s, output queue size 12
progress 25% @chr4:117000001, elapsed 0.7s, est remaining 2.0s, peak mem 851MB, user 1.7s, sys 18.2s, output queue size 2
progress 30% @chr5:88000001, elapsed 0.8s, est remaining 1.8s, peak mem 896MB, user 1.9s, sys 21.2s, output queue size 16
progress 35% @chr6:63000001, elapsed 0.9s, est remaining 1.6s, peak mem 947MB, user 2.2s, sys 24.1s, output queue size 3
progress 40% @chr7:59000001, elapsed 1.0s, est remaining 1.5s, peak mem 1001MB, user 2.5s, sys 27.1s, output queue size 6
progress 45% @chr8:58000001, elapsed 1.1s, est remaining 1.3s, peak mem 1058MB, user 2.7s, sys 30.1s, output queue size 19
progress 50% @chr9:76000001, elapsed 1.2s, est remaining 1.2s, peak mem 1127MB, user 3.0s, sys 33.0s, output queue size 15
progress 55% @chr10:96000001, elapsed 1.3s, est remaining 1.1s, peak mem 1166MB, user 3.3s, sys 36.0s, output queue size 14
progress 60% @chr11:99000001, elapsed 1.5s, est remaining 1.0s, peak mem 1220MB, user 3.6s, sys 41.1s, output queue size 24
progress 65% @chr13:39000001, elapsed 1.7s, est remaining 0.9s, peak mem 1289MB, user 4.0s, sys 46.9s, output queue size 29
progress 70% @chr14:28000001, elapsed 1.9s, est remaining 0.8s, peak mem 1349MB, user 4.3s, sys 54.1s, output queue size 33
progress 75% @chr16:5000001, elapsed 2.2s, est remaining 0.7s, peak mem 1376MB, user 4.6s, sys 61.6s, output queue size 13
progress 80% @chr17:81000001, elapsed 2.4s, est remaining 0.6s, peak mem 1406MB, user 5.0s, sys 68.5s, output queue size 8
progress 85% @chr20:18000001, elapsed 2.7s, est remaining 0.5s, peak mem 1454MB, user 5.4s, sys 75.6s, output queue size 4
progress 90% @chrX:38000001, elapsed 3.1s, est remaining 0.3s, peak mem 2735MB, user 9.3s, sys 79.6s, output queue size 114
progress 95% @chrY:32000001, elapsed 3.4s, est remaining 0.2s, peak mem 2756MB, user 12.5s, sys 83.3s, output queue size 276
progress 100% @chr21:41000001, elapsed 5.6s, est remaining 0.0s, peak mem 2759MB, user 24.7s, sys 88.3s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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: 52290604
output file size: 74586810
reads: 1001133
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.017 real
ReadQualCal::delayed_init: 1 calls 0.007 user 0.002 sys 0.018 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 1.514 user 10.839 sys 12.657 real
done: 1 calls 0.437 user 0.409 sys 0.855 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.000 sys 5.789 real
fetch: 3219322 calls 0.237 user 11.359 sys 10.316 real
fetch_reads: 3219322 calls 0.409 user 10.360 sys 10.422 real
fetch_ref: 13318 calls 0.043 user 0.033 sys 0.071 real
fetch_vcf: 13318 calls 1.066 user 0.102 sys 1.422 real
idle: 1518 calls 0.924 user 0.252 sys 118.131 real
init: 1 calls 0.010 user 0.002 sys 0.024 real
update: 13537 calls 6.704 user 2.010 sys 9.320 real
write: 3219322 calls 9.688 user 10.682 sys 20.639 real
overall: 2893594624 mem 28.446 user 89.629 sys 8.018 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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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 0.029 user 0.001 sys 0.028 real
done: 1 calls 0.059 user 0.001 sys 0.058 real
idle: 61 calls 0.002 user 0.000 sys 31.254 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81862656 mem 0.091 user 0.022 sys 1.052 real