Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/d48431c7b5765fd6f4f76ac5db2eba/1136_6G2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  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/19/ba750c622616f3ff2c15fd1c571e27/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/d48431c7b5765fd6f4f76ac5db2eba/1136_6G2-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-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-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/ba750c622616f3ff2c15fd1c571e27/.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_6G2-T1-TDNA-1_A23MHWWLT4_1.md.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed --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_6G2-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119966338, elapsed 8.4s, est remaining 159.9s, peak mem 5047MB, user 223.2s, sys 5.5s, output queue size 169
progress 10% @chr2:15945493, elapsed 15.6s, est remaining 140.0s, peak mem 5764MB, user 413.7s, sys 7.4s, output queue size 647
progress 15% @chr2:190057258, elapsed 23.1s, est remaining 130.6s, peak mem 6555MB, user 613.3s, sys 9.5s, output queue size 291
progress 20% @chr3:98497681, elapsed 31.5s, est remaining 126.1s, peak mem 6749MB, user 844.4s, sys 11.0s, output queue size 419
progress 25% @chr4:88489166, elapsed 37.8s, est remaining 113.3s, peak mem 6965MB, user 1008.1s, sys 12.5s, output queue size 101
progress 30% @chr5:147639632, elapsed 43.0s, est remaining 100.3s, peak mem 6965MB, user 1142.5s, sys 13.5s, output queue size 208
progress 35% @chr6:127143030, elapsed 52.3s, est remaining 97.1s, peak mem 7013MB, user 1393.5s, sys 15.5s, output queue size 640
progress 40% @chr7:128848793, elapsed 60.4s, est remaining 90.6s, peak mem 7206MB, user 1607.1s, sys 17.0s, output queue size 544
progress 45% @chr9:1975291, elapsed 68.9s, est remaining 84.2s, peak mem 7510MB, user 1840.1s, sys 18.6s, output queue size 27
progress 50% @chr10:32021226, elapsed 77.3s, est remaining 77.3s, peak mem 7558MB, user 2067.0s, sys 20.4s, output queue size 98
progress 55% @chr11:48978872, elapsed 84.8s, est remaining 69.4s, peak mem 7558MB, user 2267.2s, sys 21.7s, output queue size 18
progress 60% @chr12:22625164, elapsed 93.5s, est remaining 62.3s, peak mem 7558MB, user 2501.5s, sys 23.3s, output queue size 705
progress 65% @chr13:49198362, elapsed 101.5s, est remaining 54.6s, peak mem 7651MB, user 2719.2s, sys 24.8s, output queue size 550
progress 70% @chr15:43067898, elapsed 108.8s, est remaining 46.6s, peak mem 7651MB, user 2913.5s, sys 26.0s, output queue size 455
progress 75% @chr16:30766379, elapsed 117.8s, est remaining 39.3s, peak mem 7651MB, user 3163.3s, sys 27.6s, output queue size 31
progress 80% @chr17:42688462, elapsed 128.4s, est remaining 32.1s, peak mem 7651MB, user 3458.6s, sys 29.3s, output queue size 705
progress 85% @chr19:5759086, elapsed 137.3s, est remaining 24.2s, peak mem 7658MB, user 3702.8s, sys 30.9s, output queue size 408
progress 90% @chr19:55624484, elapsed 147.5s, est remaining 16.4s, peak mem 7936MB, user 3984.9s, sys 32.7s, output queue size 64
progress 95% @chr22:36504098, elapsed 157.1s, est remaining 8.3s, peak mem 7936MB, user 4247.8s, sys 34.4s, output queue size 24
progress 100% @chr6_GL000251v2_alt:3939000, elapsed 162.3s, est remaining 0.0s, peak mem 7936MB, user 4386.1s, sys 35.2s, output queue size 7
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
input file size: 56390667151
reads: 1090474054
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2206.556 user 27.715 sys 2330.474 real
done: 1 calls 0.302 user 0.579 sys 0.889 real
execute: 1 calls 0.002 user 0.011 sys 162.322 real
fetch_reads: 208647 calls 178.914 user 0.399 sys 186.952 real
fetch_ref: 207213 calls 1.053 user 1.060 sys 2.104 real
fetch_vcf: 207213 calls 81.733 user 2.208 sys 85.755 real
idle: 111 calls 0.218 user 0.000 sys 32.423 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 457992 calls 2229.678 user 2.794 sys 2300.062 real
overall: 8321716224 mem 4897.636 user 36.997 sys 163.919 real
ls: cannot access '*.table.post': No such file or directory
ls: cannot access '*.recalibrated.bam': No such file or directory
ls: cannot access '*.recalibrated.bam.bai': No such file or directory
ls: cannot access '*.csv': No such file or directory
ls: cannot access '*.pdf': No such file or directory