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/a5/5bccf33822723695cc22b7376f2be6/1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/fed4e7f1df4250cd528c23bf6e8dbf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/5bccf33822723695cc22b7376f2be6/1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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/fc/8760f164f3eb7f9ac92539edadbe66/1136_5L2-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.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/fed4e7f1df4250cd528c23bf6e8dbf/.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_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=1136_5L2-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_5L2-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:177000001, elapsed 29.6s, est remaining 561.8s, peak mem 5423MB, user 739.9s, sys 7.6s, output queue size 44
progress 10% @chr2:80000001, elapsed 52.5s, est remaining 472.5s, peak mem 7546MB, user 1472.2s, sys 11.6s, output queue size 48
progress 15% @chr2:224000001, elapsed 80.2s, est remaining 454.2s, peak mem 8659MB, user 2224.0s, sys 14.8s, output queue size 203
progress 20% @chr3:161000001, elapsed 101.3s, est remaining 405.2s, peak mem 8768MB, user 2937.6s, sys 18.7s, output queue size 141
progress 25% @chr4:134000001, elapsed 119.9s, est remaining 359.7s, peak mem 8789MB, user 3494.1s, sys 20.7s, output queue size 302
progress 30% @chr5:75000001, elapsed 135.1s, est remaining 315.2s, peak mem 8812MB, user 3958.8s, sys 22.8s, output queue size 464
progress 35% @chr6:44000001, elapsed 155.8s, est remaining 289.4s, peak mem 9132MB, user 4514.8s, sys 25.1s, output queue size 625
progress 40% @chr7:79000001, elapsed 181.9s, est remaining 272.8s, peak mem 9690MB, user 5160.8s, sys 27.3s, output queue size 786
progress 45% @chr8:82000001, elapsed 207.6s, est remaining 253.8s, peak mem 9845MB, user 6098.8s, sys 31.2s, output queue size 204
progress 50% @chr9:36000001, elapsed 230.1s, est remaining 230.1s, peak mem 10048MB, user 6686.1s, sys 34.5s, output queue size 366
progress 55% @chr10:101000001, elapsed 258.3s, est remaining 211.3s, peak mem 10263MB, user 7516.3s, sys 37.7s, output queue size 527
progress 60% @chr12:3000001, elapsed 284.9s, est remaining 189.9s, peak mem 10263MB, user 8367.3s, sys 40.6s, output queue size 510
progress 65% @chr12:111000001, elapsed 312.5s, est remaining 168.3s, peak mem 10268MB, user 9123.8s, sys 43.5s, output queue size 672
progress 70% @chr14:79000001, elapsed 330.7s, est remaining 141.7s, peak mem 10268MB, user 9724.1s, sys 45.7s, output queue size 833
progress 75% @chr16:41000001, elapsed 357.6s, est remaining 119.2s, peak mem 10268MB, user 10586.6s, sys 48.9s, output queue size 461
progress 80% @chr18:9000001, elapsed 393.7s, est remaining 98.4s, peak mem 10268MB, user 11555.1s, sys 52.1s, output queue size 623
progress 85% @chr18:47000001, elapsed 427.9s, est remaining 75.5s, peak mem 10268MB, user 12638.6s, sys 55.9s, output queue size 785
progress 90% @chrX:34000001, elapsed 448.9s, est remaining 49.9s, peak mem 10337MB, user 13417.4s, sys 59.0s, output queue size 513
progress 95% @chrY:53000001, elapsed 461.8s, est remaining 24.3s, peak mem 10349MB, user 13735.8s, sys 60.2s, output queue size 675
progress 100% @chr22:23000001, elapsed 479.8s, est remaining 0.0s, peak mem 10349MB, user 14236.0s, sys 62.4s, output queue size 3635
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: 52593107263
output file size: 82477282863
reads: 1002659546
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.020 real
ReadQualCal::delayed_init: 1 calls 0.003 user 0.001 sys 0.021 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 1161.495 user 17.204 sys 1206.128 real
done: 1 calls 0.451 user 0.340 sys 0.794 real
exec_no_coor: 1 calls 0.016 user 0.000 sys 0.021 real
execute: 1 calls 0.000 user 0.001 sys 480.519 real
fetch: 3219323 calls 62.308 user 0.354 sys 87.200 real
fetch_reads: 3219322 calls 229.359 user 0.971 sys 234.907 real
fetch_ref: 1918917 calls 6.631 user 1.388 sys 8.441 real
fetch_vcf: 1918917 calls 101.568 user 1.750 sys 106.445 real
idle: 22751 calls 9.976 user 0.138 sys 409.132 real
init: 1 calls 0.003 user 0.007 sys 0.027 real
update: 2217658 calls 3379.634 user 4.164 sys 3508.838 real
write: 3219323 calls 10638.876 user 32.489 sys 10770.900 real
overall: 10852696064 mem 14257.265 user 87.195 sys 482.812 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.table --after 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.table.post 1136_5L2-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 0.030 user 0.000 sys 0.043 real
done: 1 calls 0.079 user 0.001 sys 0.080 real
idle: 61 calls 0.002 user 0.000 sys 31.310 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86810624 mem 0.119 user 0.010 sys 1.053 real