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gatech-genemark / ProtHint

Protein hint generation pipeline for gene finding in eukaryotic genomes
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error: Alignment is missing after header #16

Closed PeiwenLi closed 4 years ago

PeiwenLi commented 4 years ago

Hi! I am running ProtHint as implemented in BRAKER2 and encountered the following non-fatal error: error: Alignment is missing after header

I think the error occurred when running the command run_spliced_alignment.pl when performing alignment with Spaln. However, the error did not stop the program. Below is the log file:

braker_38204526.log

What does it mean and what should I do about it?

Thanks, Peiwen

tomasbruna commented 4 years ago

Hello,

do not worry, about this error, this can rarely happen with Spaln, but usually, a very small number of alignments is affected (in your case, it seems to be 19 / 277028) with no effect on the final result.

I will change this message from error to warning (or maybe I'll completely suppress it) not to create this confusion.

Thanks, Tomas