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GBFF files as reference #276

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DLCrawford opened this issue Dec 10, 2024 · 0 comments
Open

GBFF files as reference #276

DLCrawford opened this issue Dec 10, 2024 · 0 comments

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@DLCrawford
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DLCrawford commented Dec 10, 2024

Hi,
Can Quast use a .gbff file as a reference genome?
I have a gbff file downloaded from NCBI and the associated gff (converted from gbff with EMBOSS).
Quast give me two errors about the reference genome:
ERROR! Skipping ./genomic.gbff because >sequence_name field is empty for the entry starting with "LOCUS CM034349".

ERROR! Reference file ./genomic.gbff is empty or contains incorrect sequences (header-only or with non-ACGTN characters)!

Can Quast use a native ".gbff? file as a reference genome?

Data:
INPUT=Pm9_combined_contigs.fasta #HiFi_asm assembly
REF=./genomic.gbff. #NCBI mussel genome
ANN =./genomic.gff #gff file from gbff mussel genome created with EMBOSS
OUTPUT=quast_out_9 # output file

Thanks
Douglas

@DLCrawford DLCrawford changed the title GBFF files GBFF files as reference Dec 10, 2024
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