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/1d/1fcf1d5d4cdf7b51d80120094af5c4/1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/1fcf1d5d4cdf7b51d80120094af5c4/1136_00H-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
  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/ec/438dda8ae93818a05f9de44f677b9e/.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-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/ec/438dda8ae93818a05f9de44f677b9e/.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_00H-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_00H-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119893964, elapsed 10.1s, est remaining 191.3s, peak mem 5597MB, user 265.9s, sys 5.8s, output queue size 178
progress 10% @chr2:21037958, elapsed 19.0s, est remaining 170.7s, peak mem 6715MB, user 502.4s, sys 8.5s, output queue size 651
progress 15% @chr2:185788643, elapsed 29.5s, est remaining 167.2s, peak mem 7692MB, user 784.3s, sys 11.2s, output queue size 271
progress 20% @chr3:98282888, elapsed 40.2s, est remaining 160.7s, peak mem 7977MB, user 1074.7s, sys 13.3s, output queue size 420
progress 25% @chr4:88463855, elapsed 48.8s, est remaining 146.4s, peak mem 8103MB, user 1301.2s, sys 15.1s, output queue size 87
progress 30% @chr5:147671678, elapsed 55.9s, est remaining 130.5s, peak mem 8275MB, user 1485.8s, sys 16.2s, output queue size 208
progress 35% @chr6:132328013, elapsed 66.9s, est remaining 124.3s, peak mem 8437MB, user 1780.2s, sys 18.2s, output queue size 638
progress 40% @chr7:102248412, elapsed 78.1s, est remaining 117.2s, peak mem 8794MB, user 2072.9s, sys 20.3s, output queue size 1416
progress 45% @chr9:1056216, elapsed 90.0s, est remaining 110.0s, peak mem 9151MB, user 2398.3s, sys 22.3s, output queue size 150
progress 50% @chr10:34359147, elapsed 100.7s, est remaining 100.7s, peak mem 9323MB, user 2689.0s, sys 24.5s, output queue size 110
progress 55% @chr11:48324941, elapsed 109.9s, est remaining 89.9s, peak mem 9323MB, user 2932.8s, sys 26.3s, output queue size 17
progress 60% @chr12:11752419, elapsed 121.2s, est remaining 80.8s, peak mem 9476MB, user 3234.2s, sys 28.5s, output queue size 810
progress 65% @chr13:49483445, elapsed 131.2s, est remaining 70.6s, peak mem 9570MB, user 3507.2s, sys 30.6s, output queue size 571
progress 70% @chr15:43135512, elapsed 140.8s, est remaining 60.3s, peak mem 9570MB, user 3762.9s, sys 32.6s, output queue size 455
progress 75% @chr16:30767894, elapsed 152.7s, est remaining 50.9s, peak mem 9570MB, user 4096.1s, sys 34.8s, output queue size 34
progress 80% @chr17:42673399, elapsed 165.4s, est remaining 41.3s, peak mem 9570MB, user 4442.4s, sys 37.3s, output queue size 702
progress 85% @chr19:5733856, elapsed 175.7s, est remaining 31.0s, peak mem 9570MB, user 4724.2s, sys 39.2s, output queue size 406
progress 90% @chr19:55817904, elapsed 186.0s, est remaining 20.7s, peak mem 9570MB, user 5005.3s, sys 41.0s, output queue size 91
progress 95% @chr22:36758311, elapsed 197.3s, est remaining 10.4s, peak mem 9627MB, user 5313.1s, sys 43.4s, output queue size 41
progress 100% @chr6_GL000254v2_alt:3881705, elapsed 203.8s, est remaining 0.0s, peak mem 9654MB, user 5484.9s, sys 44.6s, output queue size 1
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: 74522953788
reads: 1364658919
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2867.700 user 36.900 sys 2997.992 real
done: 1 calls 0.409 user 0.339 sys 0.756 real
execute: 1 calls 0.002 user 0.011 sys 203.814 real
fetch_reads: 208647 calls 242.196 user 0.550 sys 247.217 real
fetch_ref: 207388 calls 1.148 user 1.105 sys 2.153 real
fetch_vcf: 207388 calls 82.121 user 2.120 sys 86.141 real
idle: 92 calls 0.142 user 0.000 sys 33.449 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 490448 calls 2792.684 user 2.352 sys 2852.706 real
overall: 10123329536 mem 6175.241 user 45.957 sys 205.410 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