Error in running miRDeep2


Hi I am trying to run miRDeep2 for identification of miRNAs.

But its showing error miRNA reference this species file mature_osa.fa has not allowed whitespaces in its first identifier.

I checked it properly and matched with the file given in tutorial, my file is also has a same pattern. I used sed command also but issue is not resolved

Can anyone please help me

Thank you in advance





updated 2 hours ago by


written 20 days ago by


I found the same problem. I understand that I can test my input for errors with: bta_mature.fa

This is the error I got:

Error in line 1: The identifier

bta-miR-26a MIMAT0003516 Bos taurus miR-26a

contains white spaces

Please check your file for the following issues:

I.  Sequences are allowed only to comprise characters [ACGTNacgtn].
II. Identifiers are not allowed to have withespaces.

You could run inputfile > newfile
This will remove everything from the id line after the first whitespace

So by calling bta_mature.fa > bta_mature.fa.fix

I was able to run mirdeep2 without problems

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