miRDeep2 whitespaces error

miRDeep2 whitespaces error


Hi everyone,

I am trying to run miRDeep2.pl and I keep getting the following error message:

#Starting miRDeep2
[1;31mError: [0mmiRNA reference this species file miRBase_ame.fa has not allowed whitespaces in its first identifier

As far as I can tell, it doesn’t have any white spaces in its first identifier.
The first line of the file looks like this


I’ve checked manually by opening in notepad and there isn’t a whitespace hanging around at the end of the line – I also ran a script to remove any just in case.
It looks exactly the same as the .fa file given in the miRDeep2 tutorial


except that I have underscores instead of hyphens. If I change it to hyphens I get exactly the same error message.

Any suggestions?

If I don’t input a known miRNA ref file it runs OK.




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