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/7c/1261d28b23651ad47330d263af1296/.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/10/9c315bb6e7871cb298609d78a3f103/1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/a1f50050620a60e26b26f2cc7d29fb/1136_76X-T1-TDNA-1_A23MHWWLT4_1.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/1261d28b23651ad47330d263af1296/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/9c315bb6e7871cb298609d78a3f103/1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=1136_76X-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_76X-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 1136_76X-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:175000001, elapsed 28.8s, est remaining 547.8s, peak mem 5593MB, user 686.3s, sys 7.7s, output queue size 145
progress 10% @chr2:46000001, elapsed 49.9s, est remaining 448.8s, peak mem 7094MB, user 1391.2s, sys 11.5s, output queue size 117
progress 15% @chr3:3000001, elapsed 71.3s, est remaining 404.2s, peak mem 7730MB, user 2045.2s, sys 15.4s, output queue size 122
progress 20% @chr3:129000001, elapsed 92.8s, est remaining 371.2s, peak mem 7984MB, user 2676.8s, sys 17.9s, output queue size 141
progress 25% @chr4:136000001, elapsed 110.8s, est remaining 332.5s, peak mem 7984MB, user 3228.2s, sys 20.3s, output queue size 302
progress 30% @chr5:105000001, elapsed 125.1s, est remaining 291.9s, peak mem 7991MB, user 3648.4s, sys 21.8s, output queue size 464
progress 35% @chr6:70000001, elapsed 147.0s, est remaining 273.0s, peak mem 8100MB, user 4276.7s, sys 23.8s, output queue size 106
progress 40% @chr7:67000001, elapsed 169.1s, est remaining 253.7s, peak mem 8308MB, user 4915.1s, sys 26.6s, output queue size 197
progress 45% @chr8:78000001, elapsed 194.2s, est remaining 237.4s, peak mem 8407MB, user 5604.8s, sys 29.5s, output queue size 356
progress 50% @chr9:89000001, elapsed 213.8s, est remaining 213.8s, peak mem 8622MB, user 6265.3s, sys 31.7s, output queue size 187
progress 55% @chr10:115000001, elapsed 241.4s, est remaining 197.5s, peak mem 8825MB, user 7032.2s, sys 34.2s, output queue size 348
progress 60% @chr12:3000001, elapsed 269.9s, est remaining 179.9s, peak mem 8831MB, user 7956.0s, sys 37.5s, output queue size 312
progress 65% @chr13:31000001, elapsed 293.4s, est remaining 158.0s, peak mem 8831MB, user 8715.1s, sys 39.4s, output queue size 138
progress 70% @chr14:84000001, elapsed 309.4s, est remaining 132.6s, peak mem 8831MB, user 9188.6s, sys 40.8s, output queue size 299
progress 75% @chr16:42000001, elapsed 335.5s, est remaining 111.8s, peak mem 8831MB, user 9891.1s, sys 43.4s, output queue size 461
progress 80% @chr18:10000001, elapsed 376.0s, est remaining 94.0s, peak mem 8921MB, user 11071.4s, sys 47.4s, output queue size 189
progress 85% @chr19:15000001, elapsed 411.9s, est remaining 72.7s, peak mem 8973MB, user 12204.3s, sys 51.3s, output queue size 351
progress 90% @chrX:34000001, elapsed 434.1s, est remaining 48.2s, peak mem 9030MB, user 12969.4s, sys 53.7s, output queue size 78
progress 95% @chrY:54000001, elapsed 447.5s, est remaining 23.6s, peak mem 9030MB, user 13374.5s, sys 55.3s, output queue size 240
progress 100% @chr22:23000001, elapsed 478.2s, est remaining 0.0s, peak mem 9055MB, user 13785.5s, sys 57.1s, output queue size 3635
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 57443072063
output file size: 81974402254
reads: 1090378638
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.011 real
ReadQualCal::delayed_init: 1 calls 0.009 user 0.000 sys 0.022 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 1324.388 user 18.238 sys 1374.496 real
done: 1 calls 0.545 user 0.349 sys 0.901 real
exec_no_coor: 1 calls 0.009 user 0.007 sys 0.040 real
execute: 1 calls 0.007 user 0.001 sys 479.098 real
fetch: 3219323 calls 73.508 user 0.476 sys 108.975 real
fetch_reads: 3219322 calls 258.201 user 0.966 sys 264.027 real
fetch_ref: 1993219 calls 6.650 user 1.165 sys 7.900 real
fetch_vcf: 1993219 calls 98.547 user 1.691 sys 104.525 real
idle: 26168 calls 6.157 user 0.201 sys 779.446 real
init: 1 calls 0.009 user 0.000 sys 0.028 real
update: 2318154 calls 3682.158 user 3.264 sys 3815.130 real
write: 3219323 calls 9786.249 user 26.881 sys 9940.556 real
overall: 9495662592 mem 13802.843 user 83.138 sys 481.676 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1136_76X-T1-TDNA-1_A23MHWWLT4_1.table --after 1136_76X-T1-TDNA-1_A23MHWWLT4_1.table.post 1136_76X-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: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.030 user 0.000 sys 0.041 real
done: 1 calls 0.080 user 0.000 sys 0.080 real
idle: 61 calls 0.002 user 0.000 sys 31.369 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86720512 mem 0.101 user 0.033 sys 1.064 real