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/ef/1b780e82228e825cb40abaea84a098/HCC1395_tumor.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/bae461e32363e2c660756c20fc21b5/.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/f3/bae461e32363e2c660756c20fc21b5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/1b780e82228e825cb40abaea84a098/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/9c5d7ca24e41997875ac913f10d9b5/HCC1395_tumor.table
  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 HCC1395_tumor.md.bam --read_filter QualCalFilter,table=HCC1395_tumor.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 HCC1395_tumor.table.post --algo ReadWriter HCC1395_tumor.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
progress 5% @chr1:162000001, elapsed 0.3s, est remaining 5.5s, peak mem 290MB, user 0.4s, sys 7.5s, output queue size 11
progress 10% @chr2:72000001, elapsed 0.5s, est remaining 4.7s, peak mem 476MB, user 0.8s, sys 14.5s, output queue size 1
progress 15% @chr2:232000001, elapsed 0.8s, est remaining 4.4s, peak mem 601MB, user 1.2s, sys 21.7s, output queue size 6
progress 20% @chr3:154000001, elapsed 1.0s, est remaining 4.1s, peak mem 689MB, user 1.5s, sys 28.8s, output queue size 13
progress 25% @chr4:114000001, elapsed 1.2s, est remaining 3.7s, peak mem 779MB, user 2.0s, sys 35.4s, output queue size 2
progress 30% @chr5:86000001, elapsed 1.5s, est remaining 3.4s, peak mem 809MB, user 2.4s, sys 41.6s, output queue size 1
progress 35% @chr6:65000001, elapsed 1.7s, est remaining 3.1s, peak mem 877MB, user 2.9s, sys 47.6s, output queue size 4
progress 40% @chr7:56000001, elapsed 1.9s, est remaining 2.8s, peak mem 931MB, user 3.3s, sys 53.9s, output queue size 1
progress 45% @chr8:55000001, elapsed 2.1s, est remaining 2.6s, peak mem 1048MB, user 3.7s, sys 60.3s, output queue size 2
progress 50% @chr9:75000001, elapsed 2.3s, est remaining 2.3s, peak mem 1171MB, user 4.2s, sys 66.6s, output queue size 11
progress 55% @chr10:92000001, elapsed 2.5s, est remaining 2.1s, peak mem 1232MB, user 4.6s, sys 72.8s, output queue size 3
progress 60% @chr11:119000001, elapsed 2.7s, est remaining 1.8s, peak mem 1336MB, user 4.9s, sys 79.0s, output queue size 4
progress 65% @chr13:14000001, elapsed 2.9s, est remaining 1.6s, peak mem 1433MB, user 5.4s, sys 85.0s, output queue size 1
progress 70% @chr14:60000001, elapsed 3.2s, est remaining 1.4s, peak mem 1492MB, user 5.7s, sys 91.0s, output queue size 2
progress 75% @chr16:10000001, elapsed 3.4s, est remaining 1.1s, peak mem 1538MB, user 6.1s, sys 97.0s, output queue size 3
progress 80% @chr18:1, elapsed 3.6s, est remaining 0.9s, peak mem 1567MB, user 6.4s, sys 103.1s, output queue size 4
progress 85% @chr20:13000001, elapsed 3.8s, est remaining 0.7s, peak mem 1670MB, user 6.7s, sys 109.1s, output queue size 9
progress 90% @chrX:45000001, elapsed 4.3s, est remaining 0.5s, peak mem 2789MB, user 10.5s, sys 111.6s, output queue size 114
progress 95% @chrY:40000001, elapsed 4.5s, est remaining 0.2s, peak mem 2813MB, user 14.9s, sys 113.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 6.1s, est remaining 0.0s, peak mem 2834MB, user 30.8s, sys 115.9s, 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 192
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 50813910
output file size: 81484553
reads: 1001320
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.024 real
ReadQualCal::delayed_init: 1 calls 0.000 user 0.000 sys 840.140 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 2.421 user 14.537 sys 17.073 real
done: 1 calls 0.315 user 0.441 sys 0.761 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.009 user 0.000 sys 6.140 real
fetch: 3219322 calls 0.466 user 14.147 sys 14.856 real
fetch_reads: 3219322 calls 0.561 user 13.817 sys 14.992 real
fetch_ref: 11263 calls 0.047 user 0.043 sys 0.060 real
fetch_vcf: 11263 calls 1.619 user 0.070 sys 1.803 real
idle: 2281 calls 4.454 user 0.418 sys 61.830 real
init: 1 calls 0.001 user 0.000 sys 840.148 real
update: 11451 calls 10.797 user 1.155 sys 12.780 real
write: 3219322 calls 9.648 user 13.766 sys 23.841 real
overall: 2971860992 mem 41.059 user 117.325 sys 847.593 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before HCC1395_tumor.table --after HCC1395_tumor.table.post HCC1395_tumor.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 192
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.029 user 0.000 sys 0.025 real
done: 1 calls 0.051 user 0.008 sys 0.055 real
idle: 61 calls 0.002 user 0.000 sys 31.436 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 82075648 mem 0.073 user 0.042 sys 1.064 real