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/fb/4cb0b07227a92b32f16b65251f3138/1029_IWL-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/6d/ae422e06771eeefe1dfbe4dc1a440f/1029_IWL-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/10b53e4ff26763c9a33a6b5f7bc283/.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/6d/ae422e06771eeefe1dfbe4dc1a440f/1029_IWL-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/10b53e4ff26763c9a33a6b5f7bc283/.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 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.md.bam --read_filter QualCalFilter,table=1029_IWL-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 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.table.post --algo ReadWriter 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:177000001, elapsed 16.8s, est remaining 319.8s, peak mem 4183MB, user 426.0s, sys 5.3s, output queue size 42
progress 10% @chr2:79000001, elapsed 29.3s, est remaining 263.8s, peak mem 4694MB, user 820.0s, sys 7.9s, output queue size 48
progress 15% @chr2:226000001, elapsed 43.1s, est remaining 244.4s, peak mem 4926MB, user 1232.6s, sys 10.3s, output queue size 122
progress 20% @chr3:168000001, elapsed 56.2s, est remaining 224.8s, peak mem 4933MB, user 1624.4s, sys 12.2s, output queue size 141
progress 25% @chr4:124000001, elapsed 68.3s, est remaining 204.8s, peak mem 5039MB, user 1986.1s, sys 13.7s, output queue size 302
progress 30% @chr5:107000001, elapsed 77.9s, est remaining 181.8s, peak mem 5077MB, user 2301.7s, sys 15.3s, output queue size 464
progress 35% @chr6:77000001, elapsed 91.0s, est remaining 169.1s, peak mem 5107MB, user 2679.9s, sys 17.1s, output queue size 106
progress 40% @chr7:63000001, elapsed 104.3s, est remaining 156.4s, peak mem 5181MB, user 3071.4s, sys 19.0s, output queue size 195
progress 45% @chr7:102000001, elapsed 119.3s, est remaining 145.9s, peak mem 5247MB, user 3516.9s, sys 20.8s, output queue size 204
progress 50% @chr9:81000001, elapsed 130.8s, est remaining 130.8s, peak mem 5381MB, user 3867.8s, sys 22.7s, output queue size 187
progress 55% @chr10:118000001, elapsed 145.5s, est remaining 119.0s, peak mem 5447MB, user 4307.4s, sys 24.3s, output queue size 348
progress 60% @chr11:130000001, elapsed 161.1s, est remaining 107.4s, peak mem 5447MB, user 4775.5s, sys 26.1s, output queue size 510
progress 65% @chr13:26000001, elapsed 174.7s, est remaining 94.0s, peak mem 5472MB, user 5215.0s, sys 27.6s, output queue size 138
progress 70% @chr14:35000001, elapsed 184.0s, est remaining 78.9s, peak mem 5472MB, user 5529.8s, sys 28.9s, output queue size 299
progress 75% @chr16:42000001, elapsed 199.3s, est remaining 66.4s, peak mem 5472MB, user 5905.9s, sys 30.3s, output queue size 461
progress 80% @chr17:50000001, elapsed 220.7s, est remaining 55.2s, peak mem 5543MB, user 6554.0s, sys 32.6s, output queue size 189
progress 85% @chr20:18000001, elapsed 239.5s, est remaining 42.3s, peak mem 5567MB, user 7200.6s, sys 35.1s, output queue size 73
progress 90% @chr21:44000001, elapsed 252.1s, est remaining 28.0s, peak mem 5596MB, user 7573.4s, sys 36.6s, output queue size 78
progress 95% @chrY:53000001, elapsed 259.9s, est remaining 13.7s, peak mem 5598MB, user 7841.8s, sys 37.8s, output queue size 211
progress 100% @chr22:23000001, elapsed 270.8s, est remaining 0.0s, peak mem 5598MB, user 8004.8s, sys 38.8s, 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: 34430769148
output file size: 51965224527
reads: 702845646
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.016 real
ReadQualCal::delayed_init: 1 calls 0.004 user 0.001 sys 0.024 real
ReadQualCal::init: 1 calls 0.000 user 0.000 sys 0.006 real
advance: 3219322 calls 783.127 user 10.894 sys 826.490 real
done: 1 calls 0.477 user 0.375 sys 0.860 real
exec_no_coor: 1 calls 0.088 user 0.050 sys 0.153 real
execute: 1 calls 0.006 user 0.000 sys 271.412 real
fetch: 3219323 calls 30.813 user 0.496 sys 51.540 real
fetch_reads: 3219322 calls 111.255 user 0.668 sys 116.195 real
fetch_ref: 1725569 calls 4.534 user 1.152 sys 6.073 real
fetch_vcf: 1725569 calls 104.330 user 1.487 sys 109.244 real
idle: 8985 calls 2.070 user 0.056 sys 294.275 real
init: 1 calls 0.006 user 0.001 sys 0.030 real
update: 1839765 calls 1608.034 user 2.556 sys 1664.693 real
write: 3219323 calls 5571.977 user 17.338 sys 5632.889 real
overall: 5870473216 mem 8013.433 user 55.100 sys 273.716 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.table --after 1029_IWL-T1-TDNA-1_A23MHWWLT4_1.table.post 1029_IWL-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 0.040 real
done: 1 calls 0.070 user 0.000 sys 0.077 real
idle: 61 calls 0.001 user 0.000 sys 31.317 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 86720512 mem 0.100 user 0.025 sys 1.055 real