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-rnd-pltf-dev-nextflow-scratch-01/work/ba/02f43684f571c0fb9d5e9a12d94137/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.table
  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/f1/3549e6f0a3cd6883239fe71c82922c/.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-rnd-pltf-dev-nextflow-scratch-01/work/1d/3fa7431e6c620d4369640253248aa8/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  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/1d/3fa7431e6c620d4369640253248aa8/1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/3549e6f0a3cd6883239fe71c82922c/.command.run
  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 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=1136_6TL-T1-TDNA-1_A23MHWWLT4_1.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 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 24.6s, est remaining 467.9s, peak mem 4992MB, user 599.2s, sys 7.4s, output queue size 44
progress 10% @chr2:80000001, elapsed 46.1s, est remaining 414.9s, peak mem 6212MB, user 1272.6s, sys 11.0s, output queue size 79
progress 15% @chr2:232000001, elapsed 66.7s, est remaining 378.2s, peak mem 6637MB, user 1900.2s, sys 14.0s, output queue size 122
progress 20% @chr3:168000001, elapsed 84.1s, est remaining 336.2s, peak mem 6730MB, user 2458.6s, sys 16.2s, output queue size 141
progress 25% @chr4:38000001, elapsed 102.4s, est remaining 307.3s, peak mem 6776MB, user 2988.2s, sys 18.7s, output queue size 302
progress 30% @chr5:99000001, elapsed 117.8s, est remaining 274.9s, peak mem 6899MB, user 3468.5s, sys 20.8s, output queue size 464
progress 35% @chr6:76000001, elapsed 138.5s, est remaining 257.2s, peak mem 7010MB, user 4024.3s, sys 23.1s, output queue size 625
progress 40% @chr7:56000001, elapsed 160.2s, est remaining 240.2s, peak mem 7394MB, user 4701.0s, sys 25.8s, output queue size 194
progress 45% @chr7:55000001, elapsed 187.3s, est remaining 228.9s, peak mem 8114MB, user 5458.0s, sys 29.0s, output queue size 204
progress 50% @chr8:143000001, elapsed 222.7s, est remaining 222.7s, peak mem 9354MB, user 6544.5s, sys 33.8s, output queue size 187
progress 55% @chr10:96000001, elapsed 244.8s, est remaining 200.3s, peak mem 9471MB, user 7264.2s, sys 37.4s, output queue size 348
progress 60% @chr11:129000001, elapsed 262.9s, est remaining 175.3s, peak mem 9471MB, user 7874.9s, sys 39.7s, output queue size 312
progress 65% @chr13:31000001, elapsed 285.4s, est remaining 153.7s, peak mem 9471MB, user 8486.2s, sys 42.0s, output queue size 474
progress 70% @chr14:60000001, elapsed 299.5s, est remaining 128.3s, peak mem 9471MB, user 8907.0s, sys 43.7s, output queue size 635
progress 75% @chr16:42000001, elapsed 322.6s, est remaining 107.5s, peak mem 9471MB, user 9581.3s, sys 45.9s, output queue size 461
progress 80% @chr17:65000001, elapsed 353.6s, est remaining 88.4s, peak mem 9471MB, user 10367.9s, sys 48.6s, output queue size 623
progress 85% @chr19:8000001, elapsed 374.7s, est remaining 66.1s, peak mem 9471MB, user 11191.0s, sys 51.6s, output queue size 351
progress 90% @chr22:50000001, elapsed 393.2s, est remaining 43.7s, peak mem 9471MB, user 11810.1s, sys 53.8s, output queue size 513
progress 95% @chrY:54000001, elapsed 407.6s, est remaining 21.5s, peak mem 9471MB, user 12285.9s, sys 55.8s, output queue size 130
progress 100% @chrX:67000001, elapsed 436.4s, est remaining 0.0s, peak mem 9471MB, user 12628.5s, sys 57.3s, output queue size 3540
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: 44707427019
output file size: 69758869223
reads: 902411031
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.039 real
ReadQualCal::delayed_init: 1 calls 0.003 user 0.001 sys 0.023 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 1029.146 user 16.314 sys 1075.845 real
done: 1 calls 0.482 user 0.547 sys 1.035 real
exec_no_coor: 1 calls 0.011 user 0.004 sys 0.021 real
execute: 1 calls 0.004 user 0.000 sys 436.968 real
fetch: 3219323 calls 53.693 user 0.480 sys 76.797 real
fetch_reads: 3219322 calls 191.065 user 0.825 sys 197.894 real
fetch_ref: 1928581 calls 6.804 user 1.312 sys 8.084 real
fetch_vcf: 1928581 calls 103.949 user 1.789 sys 108.988 real
idle: 25690 calls 9.216 user 0.196 sys 715.121 real
init: 1 calls 0.007 user 0.001 sys 0.029 real
update: 2153881 calls 2586.704 user 4.045 sys 2675.110 real
write: 3219323 calls 9436.503 user 28.069 sys 9533.451 real
overall: 9931341824 mem 12647.519 user 78.480 sys 439.032 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.table --after 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.table.post 1136_6TL-T1-TDNA-1_A23MHWWLT4_1.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 0.020 user 0.010 sys 0.042 real
done: 1 calls 0.040 user 0.030 sys 0.078 real
idle: 61 calls 0.002 user 0.000 sys 31.294 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86794240 mem 0.070 user 0.058 sys 1.054 real