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/26/bdb804792874396554f8c9a3111296/HCC1395_tumor.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/1a61cb0673d6aed875d3e8d56c4566/.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/dc/1a61cb0673d6aed875d3e8d56c4566/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/bdb804792874396554f8c9a3111296/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/abbc3e865441056b5cbdbb57e966eb/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% @chr1:161000001, elapsed 0.1s, est remaining 2.1s, peak mem 272MB, user 0.2s, sys 2.6s, output queue size 18
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 1.8s, peak mem 446MB, user 0.4s, sys 5.0s, output queue size 9
progress 15% @chr2:230000001, elapsed 0.3s, est remaining 1.9s, peak mem 614MB, user 0.8s, sys 8.0s, output queue size 28
progress 20% @chr3:143000001, elapsed 0.6s, est remaining 2.2s, peak mem 707MB, user 1.4s, sys 14.8s, output queue size 31
progress 25% @chr4:138000001, elapsed 0.7s, est remaining 2.2s, peak mem 794MB, user 1.7s, sys 20.2s, output queue size 33
progress 30% @chr5:82000001, elapsed 0.9s, est remaining 2.1s, peak mem 824MB, user 2.2s, sys 24.9s, output queue size 24
progress 35% @chr6:47000001, elapsed 1.1s, est remaining 2.0s, peak mem 893MB, user 2.6s, sys 29.4s, output queue size 19
progress 40% @chr7:55000001, elapsed 1.1s, est remaining 1.7s, peak mem 947MB, user 2.8s, sys 32.0s, output queue size 16
progress 45% @chr8:49000001, elapsed 1.3s, est remaining 1.6s, peak mem 1106MB, user 3.1s, sys 35.4s, output queue size 65
progress 50% @chr9:71000001, elapsed 1.4s, est remaining 1.4s, peak mem 1190MB, user 3.6s, sys 40.3s, output queue size 11
progress 55% @chr10:91000001, elapsed 1.6s, est remaining 1.3s, peak mem 1247MB, user 3.9s, sys 45.2s, output queue size 20
progress 60% @chr11:121000001, elapsed 1.8s, est remaining 1.2s, peak mem 1295MB, user 4.2s, sys 50.1s, output queue size 26
progress 65% @chr13:10000001, elapsed 2.0s, est remaining 1.1s, peak mem 1361MB, user 4.6s, sys 56.3s, output queue size 14
progress 70% @chr14:70000001, elapsed 2.3s, est remaining 1.0s, peak mem 1433MB, user 5.0s, sys 63.6s, output queue size 23
progress 75% @chr16:17000001, elapsed 2.5s, est remaining 0.8s, peak mem 1469MB, user 5.3s, sys 70.9s, output queue size 22
progress 80% @chr18:3000001, elapsed 2.7s, est remaining 0.7s, peak mem 1499MB, user 5.6s, sys 78.1s, output queue size 23
progress 85% @chr20:24000001, elapsed 3.0s, est remaining 0.5s, peak mem 1622MB, user 6.1s, sys 85.1s, output queue size 25
progress 90% @chrX:41000001, elapsed 3.5s, est remaining 0.4s, peak mem 2759MB, user 10.0s, sys 89.0s, output queue size 114
progress 95% @chrY:36000001, elapsed 3.7s, est remaining 0.2s, peak mem 2780MB, user 13.8s, sys 92.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 6.3s, est remaining 0.0s, peak mem 2795MB, user 27.5s, sys 97.5s, 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: 50813912
output file size: 81484557
reads: 1001320
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.025 real
ReadQualCal::delayed_init: 1 calls 0.005 user 0.002 sys 0.022 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 1.887 user 11.833 sys 14.089 real
done: 1 calls 0.365 user 0.882 sys 1.251 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.000 sys 6.408 real
fetch: 3219322 calls 0.297 user 11.471 sys 12.023 real
fetch_reads: 3219322 calls 0.404 user 11.839 sys 12.138 real
fetch_ref: 11263 calls 0.049 user 0.020 sys 0.063 real
fetch_vcf: 11263 calls 1.127 user 0.133 sys 1.377 real
idle: 1916 calls 1.438 user 0.283 sys 128.627 real
init: 1 calls 0.007 user 0.002 sys 0.028 real
update: 11451 calls 6.534 user 2.077 sys 9.510 real
write: 3219322 calls 11.482 user 11.355 sys 23.399 real
overall: 2931085312 mem 32.142 user 99.499 sys 8.769 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 384
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.030 user 0.000 sys 0.024 real
done: 1 calls 0.040 user 0.010 sys 0.055 real
idle: 60 calls 0.002 user 0.000 sys 31.402 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81944576 mem 0.068 user 0.045 sys 1.055 real