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/14/de14d1288827a7d870211563ddef46/HCC1395_tumor.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/81a0bbd77c18e74eacd36ee2826f96/.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/5c/81a0bbd77c18e74eacd36ee2826f96/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/de14d1288827a7d870211563ddef46/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/36f0bc0a1ffd2640e153f1f58346d5/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.
progress 5% @chr1:188000001, elapsed 0.2s, est remaining 3.8s, peak mem 268MB, user 0.5s, sys 4.9s, output queue size 7
progress 10% @chr2:67000001, elapsed 0.4s, est remaining 3.3s, peak mem 391MB, user 0.7s, sys 9.9s, output queue size 20
progress 15% @chr2:233000001, elapsed 0.5s, est remaining 3.1s, peak mem 577MB, user 1.0s, sys 14.9s, output queue size 20
progress 20% @chr3:173000001, elapsed 0.7s, est remaining 2.8s, peak mem 670MB, user 1.4s, sys 19.7s, output queue size 12
progress 25% @chr4:98000001, elapsed 0.9s, est remaining 2.7s, peak mem 736MB, user 1.8s, sys 24.6s, output queue size 18
progress 30% @chr5:111000001, elapsed 1.1s, est remaining 2.6s, peak mem 772MB, user 2.1s, sys 31.0s, output queue size 24
progress 35% @chr6:50000001, elapsed 1.3s, est remaining 2.5s, peak mem 832MB, user 2.4s, sys 37.6s, output queue size 24
progress 40% @chr7:79000001, elapsed 1.6s, est remaining 2.3s, peak mem 874MB, user 2.8s, sys 44.2s, output queue size 17
progress 45% @chr8:82000001, elapsed 1.8s, est remaining 2.2s, peak mem 982MB, user 3.2s, sys 51.1s, output queue size 24
progress 50% @chr9:55000001, elapsed 2.0s, est remaining 2.0s, peak mem 1063MB, user 3.6s, sys 58.4s, output queue size 40
progress 55% @chr10:79000001, elapsed 2.3s, est remaining 1.9s, peak mem 1108MB, user 4.0s, sys 65.3s, output queue size 16
progress 60% @chr11:108000001, elapsed 2.5s, est remaining 1.7s, peak mem 1177MB, user 4.3s, sys 72.2s, output queue size 15
progress 65% @chr12:122000001, elapsed 2.8s, est remaining 1.5s, peak mem 1243MB, user 4.7s, sys 79.2s, output queue size 33
progress 70% @chr14:73000001, elapsed 3.0s, est remaining 1.3s, peak mem 1321MB, user 5.1s, sys 86.6s, output queue size 18
progress 75% @chr16:5000001, elapsed 3.2s, est remaining 1.1s, peak mem 1369MB, user 5.5s, sys 93.7s, output queue size 13
progress 80% @chr18:10000001, elapsed 3.5s, est remaining 0.9s, peak mem 1390MB, user 5.8s, sys 100.4s, output queue size 18
progress 85% @chr20:11000001, elapsed 3.7s, est remaining 0.7s, peak mem 1528MB, user 6.3s, sys 107.5s, output queue size 18
progress 90% @chrX:38000001, elapsed 4.2s, est remaining 0.5s, peak mem 2749MB, user 10.2s, sys 111.0s, output queue size 114
progress 95% @chrY:44000001, elapsed 4.4s, est remaining 0.2s, peak mem 2770MB, user 14.4s, sys 114.5s, output queue size 276
progress 100% @chr21:41000001, elapsed 7.0s, est remaining 0.0s, peak mem 2791MB, user 28.0s, sys 119.0s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 50813900
output file size: 81484548
reads: 1001320
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.017 sys 0.028 real
ReadQualCal::delayed_init: 1 calls 0.004 user 0.001 sys 0.026 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 1.784 user 16.054 sys 16.393 real
done: 1 calls 0.354 user 0.321 sys 0.677 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.002 sys 7.086 real
fetch: 3219322 calls 0.261 user 14.787 sys 13.132 real
fetch_reads: 3219322 calls 0.377 user 15.453 sys 13.233 real
fetch_ref: 11263 calls 0.059 user 0.036 sys 0.084 real
fetch_vcf: 11263 calls 1.123 user 0.142 sys 1.399 real
idle: 1929 calls 1.321 user 0.386 sys 96.893 real
init: 1 calls 0.004 user 0.001 sys 0.032 real
update: 11451 calls 7.117 user 1.618 sys 9.605 real
write: 3219322 calls 11.436 user 15.290 sys 25.097 real
overall: 2927550464 mem 32.556 user 120.529 sys 8.425 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 6.12.83
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 0.025 real
done: 1 calls 0.050 user 0.010 sys 0.054 real
idle: 61 calls 0.003 user 0.000 sys 31.465 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81895424 mem 0.068 user 0.045 sys 1.061 real