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/ac/6b349e5e1590c1ab5d50dfabd251ac/Sig_18_Blood.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/e04f013b5266d6b8acb979791f0560/.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/17/e04f013b5266d6b8acb979791f0560/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/1522110040efeb211ec882b01ba433/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/1522110040efeb211ec882b01ba433/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% @chr1:164000001, elapsed 0.2s, est remaining 4.2s, peak mem 304MB, user 0.5s, sys 5.7s, output queue size 1
progress 10% @chr2:75000001, elapsed 0.4s, est remaining 3.7s, peak mem 496MB, user 0.9s, sys 11.1s, output queue size 41
progress 15% @chr2:230000001, elapsed 0.6s, est remaining 3.4s, peak mem 607MB, user 1.1s, sys 16.7s, output queue size 5
progress 20% @chr3:159000001, elapsed 0.8s, est remaining 3.1s, peak mem 730MB, user 1.5s, sys 21.9s, output queue size 18
progress 25% @chr4:115000001, elapsed 1.0s, est remaining 2.9s, peak mem 829MB, user 1.7s, sys 27.4s, output queue size 14
progress 30% @chr5:110000001, elapsed 1.2s, est remaining 2.7s, peak mem 922MB, user 1.9s, sys 33.4s, output queue size 12
progress 35% @chr6:51000001, elapsed 1.4s, est remaining 2.7s, peak mem 967MB, user 2.2s, sys 41.5s, output queue size 14
progress 40% @chr7:44000001, elapsed 1.7s, est remaining 2.6s, peak mem 1015MB, user 2.5s, sys 49.8s, output queue size 14
progress 45% @chr8:48000001, elapsed 2.0s, est remaining 2.5s, peak mem 1117MB, user 2.8s, sys 58.4s, output queue size 65
progress 50% @chr9:66000001, elapsed 2.3s, est remaining 2.3s, peak mem 1204MB, user 3.1s, sys 66.9s, output queue size 11
progress 55% @chr10:111000001, elapsed 2.6s, est remaining 2.1s, peak mem 1273MB, user 3.5s, sys 75.3s, output queue size 11
progress 60% @chr11:118000001, elapsed 2.9s, est remaining 1.9s, peak mem 1336MB, user 3.7s, sys 83.7s, output queue size 21
progress 65% @chr13:8000001, elapsed 3.1s, est remaining 1.7s, peak mem 1414MB, user 4.0s, sys 92.2s, output queue size 7
progress 70% @chr14:46000001, elapsed 3.4s, est remaining 1.5s, peak mem 1459MB, user 4.3s, sys 100.5s, output queue size 15
progress 75% @chr16:10000001, elapsed 3.7s, est remaining 1.2s, peak mem 1537MB, user 4.6s, sys 108.9s, output queue size 12
progress 80% @chr17:78000001, elapsed 4.0s, est remaining 1.0s, peak mem 1564MB, user 4.8s, sys 117.1s, output queue size 6
progress 85% @chr20:32000001, elapsed 4.2s, est remaining 0.7s, peak mem 1600MB, user 5.2s, sys 125.2s, output queue size 10
progress 90% @chrX:40000001, elapsed 4.8s, est remaining 0.5s, peak mem 2755MB, user 9.7s, sys 129.7s, output queue size 114
progress 95% @chrY:39000001, elapsed 5.0s, est remaining 0.3s, peak mem 2773MB, user 12.5s, sys 133.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 7.1s, est remaining 0.0s, peak mem 2776MB, user 24.9s, sys 139.8s, 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: 52290599
output file size: 74586799
reads: 1001133
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.012 real
ReadQualCal::delayed_init: 1 calls 0.002 user 0.000 sys 0.025 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 1.694 user 17.624 sys 19.284 real
done: 1 calls 0.331 user 0.371 sys 0.705 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.004 user 0.000 sys 7.172 real
fetch: 3219322 calls 0.278 user 16.704 sys 16.756 real
fetch_reads: 3219322 calls 0.230 user 17.132 sys 16.824 real
fetch_ref: 13318 calls 0.044 user 0.052 sys 0.089 real
fetch_vcf: 13318 calls 1.312 user 0.150 sys 1.611 real
idle: 1430 calls 0.747 user 0.237 sys 106.746 real
init: 1 calls 0.006 user 0.000 sys 0.031 real
update: 13537 calls 6.745 user 1.729 sys 9.353 real
write: 3219322 calls 9.727 user 16.819 sys 27.468 real
overall: 2911244288 mem 27.928 user 141.160 sys 9.270 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 0.019 user 0.001 sys 0.027 real
done: 1 calls 0.046 user 0.004 sys 0.057 real
idle: 61 calls 0.002 user 0.000 sys 31.426 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81944576 mem 0.078 user 0.031 sys 1.056 real