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-rnd-pltf-dev-nextflow-scratch-01/work/45/3242095800e1c7dce8187cd945d1df/659_bR4-T1-TDNA-1_A23MHWWLT4_1.table
  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/fc/d5146d4d65fe6797fcdc1bb7680930/.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/8c/fd9d16d5f12b5a7d5c9a20f5f532db/659_bR4-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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/8c/fd9d16d5f12b5a7d5c9a20f5f532db/659_bR4-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/d5146d4d65fe6797fcdc1bb7680930/.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 659_bR4-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=659_bR4-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 659_bR4-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 659_bR4-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:153000001, elapsed 38.8s, est remaining 738.0s, peak mem 7485MB, user 948.9s, sys 10.4s, output queue size 44
progress 10% @chr2:70000001, elapsed 73.7s, est remaining 663.6s, peak mem 11794MB, user 2017.5s, sys 16.4s, output queue size 79
progress 15% @chr3:18000001, elapsed 110.6s, est remaining 626.8s, peak mem 13038MB, user 3045.0s, sys 21.4s, output queue size 203
progress 20% @chr3:176000001, elapsed 139.2s, est remaining 557.0s, peak mem 13045MB, user 3988.8s, sys 27.0s, output queue size 218
progress 25% @chr4:124000001, elapsed 165.2s, est remaining 495.7s, peak mem 13293MB, user 4809.1s, sys 30.6s, output queue size 302
progress 30% @chr5:107000001, elapsed 188.6s, est remaining 440.1s, peak mem 13459MB, user 5532.5s, sys 33.7s, output queue size 464
progress 35% @chr6:91000001, elapsed 217.3s, est remaining 403.6s, peak mem 13694MB, user 6306.7s, sys 37.0s, output queue size 625
progress 40% @chr7:47000001, elapsed 249.7s, est remaining 374.6s, peak mem 13714MB, user 7176.9s, sys 40.4s, output queue size 786
progress 45% @chr8:72000001, elapsed 287.2s, est remaining 351.1s, peak mem 13728MB, user 8474.3s, sys 44.9s, output queue size 204
progress 50% @chr8:144000001, elapsed 318.8s, est remaining 318.8s, peak mem 14143MB, user 9282.7s, sys 47.6s, output queue size 366
progress 55% @chr10:109000001, elapsed 355.1s, est remaining 290.6s, peak mem 14288MB, user 10396.0s, sys 51.7s, output queue size 527
progress 60% @chr11:134000001, elapsed 389.7s, est remaining 259.8s, peak mem 14288MB, user 11494.0s, sys 55.8s, output queue size 510
progress 65% @chr13:26000001, elapsed 429.1s, est remaining 231.0s, peak mem 14288MB, user 12537.1s, sys 59.5s, output queue size 672
progress 70% @chr14:60000001, elapsed 453.3s, est remaining 194.3s, peak mem 14416MB, user 13393.7s, sys 62.4s, output queue size 833
progress 75% @chr16:42000001, elapsed 489.5s, est remaining 163.2s, peak mem 14644MB, user 14312.9s, sys 65.7s, output queue size 995
progress 80% @chr17:58000001, elapsed 541.7s, est remaining 135.4s, peak mem 14678MB, user 15849.0s, sys 70.7s, output queue size 623
progress 85% @chr20:23000001, elapsed 589.6s, est remaining 104.0s, peak mem 14711MB, user 17577.5s, sys 76.6s, output queue size 351
progress 90% @chrX:35000001, elapsed 619.3s, est remaining 68.8s, peak mem 15150MB, user 18505.6s, sys 80.0s, output queue size 513
progress 95% @chrY:54000001, elapsed 638.5s, est remaining 33.6s, peak mem 15150MB, user 19134.6s, sys 82.6s, output queue size 240
progress 100% @chr22:23000001, elapsed 672.9s, est remaining 0.0s, peak mem 15359MB, user 19810.9s, sys 85.4s, 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: 83203675103
output file size: 121116513213
reads: 1632923217
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.033 real
ReadQualCal::delayed_init: 1 calls 0.008 user 0.000 sys 0.023 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 1843.860 user 25.836 sys 1906.666 real
done: 1 calls 0.499 user 0.421 sys 0.920 real
exec_no_coor: 1 calls 0.000 user 0.023 sys 0.025 real
execute: 1 calls 0.006 user 0.001 sys 674.074 real
fetch: 3219323 calls 108.333 user 0.464 sys 149.224 real
fetch_reads: 3219322 calls 341.765 user 1.458 sys 349.623 real
fetch_ref: 1996753 calls 7.646 user 1.169 sys 9.085 real
fetch_vcf: 1996753 calls 100.349 user 1.713 sys 105.376 real
idle: 45215 calls 15.022 user 0.539 sys 751.826 real
init: 1 calls 0.008 user 0.000 sys 0.029 real
update: 2342641 calls 3806.713 user 3.730 sys 3953.854 real
write: 3219323 calls 15117.829 user 45.861 sys 15292.906 real
overall: 16106008576 mem 19839.695 user 122.662 sys 676.681 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 659_bR4-T1-TDNA-1_A23MHWWLT4_1.table --after 659_bR4-T1-TDNA-1_A23MHWWLT4_1.table.post 659_bR4-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 0.058 user 0.001 sys 0.052 real
done: 1 calls 0.088 user 0.011 sys 0.102 real
idle: 61 calls 0.003 user 0.000 sys 31.265 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 83648512 mem 0.129 user 0.032 sys 1.056 real