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lorrainea / MARS

MARS: improving Multiple circular sequence Alignment using Refined Sequences
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contains an unexpected character #12

Closed ejna1212 closed 4 weeks ago

ejna1212 commented 1 year ago

Hello,

I am trying to run MARs using multiple circovirus genomes (DNA sequences). Each sequence is composed of A, T, G, and C, and some sequences also include N in the middle. However, when I try to run my FASTA file in MARS, it gives an error message saying "contains an unexpected character".

Running the command as shown in the examples, "./mars -a DNA -m 0 -i ./data/10.gappy.fasta -o ./data/10.gappy.output.fasta -q 5 -l 20 -P 1," works. However, when I try to run "mammals.bear.fas" in the "exp2" folder, I encounter the same "contains an unexpected character" error. What are differences between "mammals.fas" and "mammals.bear.fas" ?

Also, how do I modify my file to make it?

Thank you!

lorrainea commented 1 year ago

Hello, I have run MARS with the mammals.bear.fas file (although this is technically an already rotated set output by the BEAR tool) it should still be able to run and successfully does for myself. I suspect this is an encoding issue and wanted to point you to this thread to see if the last comment solves your problem https://github.com/lorrainea/MARS/issues/2.

Regards Lorraine