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TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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Bug when using soft link to genome #102

Closed mylena-s closed 6 months ago

mylena-s commented 6 months ago

Hello! I am writing to report a small bug of EarlGrey when you use as input a symbolic link pointing to the genome rather than a fasta file.

The following error appears

"Command line fasta file *.fasta.prep does not exist!
BLAST Database error: No alias or index file found for nucleotide database " and the database directory is empty.

The error message is not informative of the bug, since there was no way to know that the cause of the error was the symbolic link, which happened before the BLAST step.

I hope this report helps to other people facing the same issue, as is a really common practice to use symbolic links rather than the original fasta file to run genomic pipelines.

Cheers

TobyBaril commented 6 months ago

Thanks for highlighting this! A small oversight on my part - fixed and pushed in release 4.2.2. This might take some time to show up in anaconda