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Old 07-12-2016, 05:31 AM   #1
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Location: Corner Brook

Join Date: Feb 2016
Posts: 8
Default Problem with mirdeep2

I have a problem with when i input my fasta file containing the reads.

here is the command and the error that i get: N1_S1.fa -c -p ~/Desktop/bowtiebuild/cod_index -m -s /home/Desktop/cod/collapsed_reads/N1_S1_collapsed.fa -t ~/Desktop/cod/arf_files/N1_S1.arf

First line of FASTA reads file is not in accordance with the fasta format specifications
Please make sure your file is in accordance with the fasta format specifications and does not contain whitespace in IDs or sequences

***** Please check if the option you used (options c) designates the correct format of the supplied reads file N1_S1.fa *****

Here are the first few lines of my FASTA file:

>@NS500451:29:H3T2FBGXX:1:11101:15273:1059 1:N:0:ATCACG
>@NS500451:29:H3T2FBGXX:1:11101:21477:1064 1:N:0:ATCACG
>@NS500451:29:H3T2FBGXX:1:11101:23355:1065 1:N:0:ATCACG

The command that i sued to convert fastq to fasta file is

awk 'NR % 4 == 1 {print ">" $0 } NR % 4 == 2 {print $0}' ~/Desktop/N1_S1_trimmed.fastq > ~/Desktop/N1_S1.fa

Important note: I had this problem when i was using mirdeep2 script in the linux server. But in my own linux machine the generated the collapsed reads and the arf files without any error code. So if there are whitespaces in the identifiers, how come the script doesn't generate any errors when i run in my own linux machine but not in the server?

Do anyone know how to fix this problem?
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