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/a2/37e6aebc954e884d428be1e5049d1b/.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/fd/1bd03d488a8acdab8cc868bc0ab154/1136_27F-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/37e6aebc954e884d428be1e5049d1b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/1bd03d488a8acdab8cc868bc0ab154/1136_27F-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  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_27F-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_27F-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119893964, elapsed 12.8s, est remaining 242.5s, peak mem 7049MB, user 352.4s, sys 7.3s, output queue size 171
progress 10% @chr2:21001730, elapsed 25.0s, est remaining 224.6s, peak mem 8651MB, user 696.8s, sys 10.7s, output queue size 651
progress 15% @chr2:185788643, elapsed 36.6s, est remaining 207.1s, peak mem 10024MB, user 1020.8s, sys 13.8s, output queue size 255
progress 20% @chr3:98588713, elapsed 48.8s, est remaining 195.3s, peak mem 10024MB, user 1367.0s, sys 16.1s, output queue size 416
progress 25% @chr4:88521888, elapsed 58.2s, est remaining 174.6s, peak mem 10024MB, user 1623.6s, sys 17.9s, output queue size 88
progress 30% @chr5:147418447, elapsed 65.7s, est remaining 153.4s, peak mem 10024MB, user 1825.1s, sys 19.1s, output queue size 197
progress 35% @chr6:132372830, elapsed 79.9s, est remaining 148.4s, peak mem 10548MB, user 2225.8s, sys 22.3s, output queue size 637
progress 40% @chr7:130070644, elapsed 98.4s, est remaining 147.5s, peak mem 30461MB, user 2686.2s, sys 30.7s, output queue size 4371
progress 45% @chr9:4990502, elapsed 115.5s, est remaining 141.2s, peak mem 43177MB, user 3143.0s, sys 39.3s, output queue size 13708
progress 50% @chr10:37136607, elapsed 128.6s, est remaining 128.6s, peak mem 44288MB, user 3549.0s, sys 47.6s, output queue size 23600
progress 55% @chr11:55650904, elapsed 140.2s, est remaining 114.7s, peak mem 45046MB, user 3859.2s, sys 49.6s, output queue size 33970
progress 60% @chr12:26580027, elapsed 154.6s, est remaining 103.1s, peak mem 45115MB, user 4246.5s, sys 51.7s, output queue size 43672
progress 65% @chr13:50015494, elapsed 167.5s, est remaining 90.2s, peak mem 45136MB, user 4596.7s, sys 54.3s, output queue size 54641
progress 70% @chr15:43178607, elapsed 178.9s, est remaining 76.7s, peak mem 45136MB, user 4988.1s, sys 60.4s, output queue size 455
progress 75% @chr16:30953185, elapsed 193.2s, est remaining 64.4s, peak mem 45136MB, user 5398.9s, sys 62.9s, output queue size 30
progress 80% @chr17:42614844, elapsed 210.2s, est remaining 52.5s, peak mem 45136MB, user 5891.1s, sys 66.1s, output queue size 125
progress 85% @chr19:5766103, elapsed 223.9s, est remaining 39.5s, peak mem 45136MB, user 6278.9s, sys 69.1s, output queue size 411
progress 90% @chr19:55881470, elapsed 236.4s, est remaining 26.3s, peak mem 45136MB, user 6634.3s, sys 71.2s, output queue size 45
progress 95% @chr22:36300851, elapsed 251.1s, est remaining 13.2s, peak mem 45136MB, user 7055.0s, sys 73.8s, output queue size 26
progress 100% @chrY:25622443, elapsed 259.2s, est remaining 0.0s, peak mem 45136MB, user 7280.9s, sys 75.0s, output queue size 31
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: 99749239266
reads: 2068464941
contig: 201779 intervals 37922265 bases
advance: 208647 calls 3905.210 user 66.145 sys 4100.295 real
done: 1 calls 0.364 user 0.410 sys 0.777 real
execute: 1 calls 0.006 user 0.002 sys 259.235 real
fetch_reads: 208647 calls 403.548 user 1.053 sys 413.344 real
fetch_ref: 207259 calls 1.258 user 0.917 sys 2.322 real
fetch_vcf: 207259 calls 84.631 user 2.160 sys 87.715 real
idle: 92 calls 0.135 user 0.000 sys 32.404 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 633812 calls 3167.065 user 2.670 sys 3254.524 real
overall: 47329153024 mem 7838.656 user 77.255 sys 261.616 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