mirdeep2 error in sequence file

Question

[kamyasingh2490]

Hi,

I am trying to identify miRNA from fastq file. I am using miRDeep2 for this purpose. As mentioned in the in the tutorial regarding the mature and precursor sequences of miRNA, I have downloaded it from miRBase version 21. While running the mirdeep2.pl command im getting this error in the report.log file.

" #Starting miRDeep2 /home/titan4/mirdeep2_0_0_8/src/miRDeep2.pl reads_collapsed.fa hg38.fa reads_collapsed_vs_genome.arf mature_new.fa none precursor_new.fa -t H.sapiens

miRDeep2 started at 12:3:54

mkdir mirdeep_runs/run_24_06_2016_t_12_03_54

testing input files

started: 12:3:54 sanity_check_mature_ref.pl mature_new.fa

Error: problem with mature_new.fa Error in line 5.177: The sequence

contains characters others than [acgtunACGTUN]

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.

Can some one help.

[sarah.deraedt]

Did you ever find the solution to this problem? I am running into pretty much the same error:

ESC[1;31mError: ESC[0mproblem with mature_dme21.fa perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C").

I have checked the files for formatting, whitespaces, and allowed characters and they are all fine. Our system administrator says the perl warning is fine and usually it does allow me to just run a program no problem. I just am stuck, and do not know what the issue could be with my mature.fa file, can anyone help?

Answer 1

[gzl]

you should check your mature.fa file. There should be only ACTGNactgn characters in the sequence lines and there should be no white spaces in the header lines. Use extract_miRNAs.pl of miRDeep2 to fetch mature miRNAs from miRBase. If you are still getting this error there may be some perl issue. Follow this link to deal with perl related issue: https://biosupport.se/p/751/ I hope this will help.