No whitespace in my .fa, yet I get a whitespace error in miRDeep2.pl

[timdelory]

I am running miRDeep2.pl on a species for which I have a FASTA of known mature miRNAs. However, I am unable to run this script successfully, as I keep receiving a whitespace error: my_mature_mirna.fa "has not allowed whitespaces in its first identifier" There are no trailing whitespaces in this fasta. I removed any potential spaces using sed -i 's/ //g', just to be sure (it did not change the file size). Here are the first few headers, perhaps something about the header names are causing an error? Thank you for your time!

GL985793_7038 TGAGATCATTGTGAAAGCTGATT GL986159_20383 TGGAATGTAAAGAAGTATGGAG GL985803_8126 ATATTGTCCTGTCACAGCAGTAC GL985734_3508 TGAGATTCAACTCCTCCAACTT GL985752_4957 TGAGTATTAATTCAGGTACTGGT

[mschilli87]

Can you pipe your FASTA file through od -c to check for non-printable characters? What kind of linebreaks does the file use (\n/\r\n)?

[timdelory]

Here is the head and tail of this your pipe request: [u60243]$ cat my_mature.fa | od -c | head 0000000 > G L 9 8 5 7 9 3 7 0 3 8 \r \n 0000020 T G A G A T C A T T G T G A A A 0000040 G C T G A T T \r \n > G L 9 8 6 1 0000060 5 9 2 0 3 8 3 \r \n T G G A A T 0000100 G T A A A G A A G T A T G G A G 0000120 \r \n > G L 9 8 5 8 0 3 8 1 2 6 0000140 \r \n A T A T T G T C C T G T C A 0000160 C A G C A G T A C \r \n > G L 9 8 0000200 5 7 3 4 3 5 0 8 \r \n T G A G A 0000220 T T C A A C T C C T C C A A C T [u60243]$ cat my_mature.fa | od -c | tail 0007440 A T A T C C G T T G A T C G T A 0007460 G T \r \n > G L 9 8 6 7 0 2 2 5 0007500 1 1 3 \r \n A G G T A A T C G T C 0007520 G G T G T T T T C G \r \n > G L 9 0007540 8 5 8 3 8 1 0 2 9 1 \r \n T C T 0007560 C A C T A T C T T G T C T T T C 0007600 A T C \r \n > G L 9 8 5 9 4 1 _ 1 0007620 4 2 5 6 \r \n C T T T G G T A A T 0007640 A C A G C T C T A T G A \r \n

[timdelory]

The problem must be that I have \r\n breaks instead of \n breaks. I will follow up after re-formating.

[timdelory]

Thank you! that was the issue.