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/d8/206bf5dd2f671b6b683916f20cdabf/.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/d8/206bf5dd2f671b6b683916f20cdabf/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/e8f9452ffe2420eb8808ba1556b1dd/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/e8f9452ffe2420eb8808ba1556b1dd/Sig_18_Blood.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 Sig_18_Blood.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 Sig_18_Blood.table
This software is licensed to bgold@natera.com by Sentieon Inc.
No more license available for sentieon:QualCal
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progress 5% @chr1:119893964, elapsed 840.2s, est remaining 15963.0s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 120
progress 10% @chr2:20224802, elapsed 840.2s, est remaining 7561.9s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 1849
progress 15% @chr2:189036616, elapsed 840.3s, est remaining 4761.5s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 12235
progress 20% @chr3:97871842, elapsed 840.3s, est remaining 3361.2s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 4605
progress 25% @chr4:88442234, elapsed 840.4s, est remaining 2521.1s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 14869
progress 30% @chr5:147383890, elapsed 840.4s, est remaining 1960.9s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 24907
progress 35% @chr6:126011192, elapsed 840.5s, est remaining 1560.8s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 180
progress 40% @chr7:128774498, elapsed 840.5s, est remaining 1260.7s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 9678
progress 45% @chr9:742205, elapsed 840.5s, est remaining 1027.3s, peak mem 283MB, user 0.0s, sys 0.0s, output queue size 19043
progress 50% @chr10:32463017, elapsed 840.6s, est remaining 840.6s, peak mem 292MB, user 0.0s, sys 0.0s, output queue size 28986
progress 55% @chr11:48263861, elapsed 840.6s, est remaining 687.8s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 39449
progress 60% @chr12:21646899, elapsed 840.7s, est remaining 560.5s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 48996
progress 65% @chr13:49278350, elapsed 840.7s, est remaining 452.7s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 60052
progress 70% @chr15:42684116, elapsed 840.8s, est remaining 360.3s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 70088
progress 75% @chr16:30942375, elapsed 840.8s, est remaining 280.3s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 79652
progress 80% @chr17:42310507, elapsed 840.9s, est remaining 210.2s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 90341
progress 85% @chr19:5678551, elapsed 841.0s, est remaining 148.4s, peak mem 333MB, user 0.0s, sys 0.1s, output queue size 7633
progress 90% @chr19:55712420, elapsed 841.0s, est remaining 93.4s, peak mem 333MB, user 0.0s, sys 0.1s, output queue size 17130
progress 95% @chr22:37066826, elapsed 841.4s, est remaining 44.3s, peak mem 2526MB, user 6.9s, sys 2.4s, output queue size 3250
progress 100% @chrY:24859666, elapsed 841.4s, est remaining 0.0s, peak mem 2526MB, user 7.1s, sys 2.4s, output queue size 1113
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: 52290604
reads: 1001133
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.819 user 0.131 sys 2.357 real
done: 1 calls 0.324 user 0.078 sys 0.405 real
execute: 1 calls 0.007 user 0.002 sys 841.444 real
fetch_reads: 208647 calls 0.147 user 0.005 sys 0.184 real
fetch_ref: 2072 calls 0.007 user 0.011 sys 0.021 real
fetch_vcf: 2072 calls 0.825 user 0.052 sys 1.013 real
idle: 61 calls 0.002 user 0.001 sys 31.019 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2257 calls 5.219 user 2.155 sys 7.913 real
overall: 2649001984 mem 10.643 user 10.459 sys 842.805 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