Problem with miRDeep2.pl

Question

[JulianC]

Hi everyone!

I have a problem with miRNA prediction analysis with miRDeep2. I have just run the mapper module and it worked well. When I use the miRDeep2.pl module, I got this error:

Error: problem with reads_collapsed.fa
/usr/bin/env: "perl -W": file or directory not found

Can anyone help me with this issue? Thanks in advance!

[ATpoint]

The questions lacks details. Please provide the full command line. Also please consider to go through How To Ask Good Questions On Technical And Scientific Forums

[JulianC]

/home/aga/Scrivania/SimoneF/miRDeep2.pl reads_collapsed_prova.fa equcab3_220218.fa reads_vs_refdb_prova_refcancellate.arf none none none

I generated the .fa and the .arf files with the mapper module. The error I got comes from this command

[GenoMax]

Do you have a file called reads_collapsed.fa in the directory you are running the command in?

[JulianC]

    aga@THOR:~/Scrivania/SimoneF/mirdeep2-master/src$ /home/aga/Scrivania/SimoneF/miRDeep2.pl reads_collapsed_prova.fa equcab3_220218.fa reads_vs_refdb_prova_refcancellate.arf none none none 


#####################################
#                                   #
# miRDeep2.0.0.8                    #
#                                   #
# last change: 20/06/2017           #
#                                   #
#####################################

miRDeep2 started at 16:4:31


#Starting miRDeep2
#Starting miRDeep2
/home/aga/Scrivania/SimoneF/miRDeep2.pl reads_collapsed_prova.fa equcab3_220218.fa reads_vs_refdb_prova_refcancellate.arf none none none

miRDeep2 started at 16:4:31


mkdir mirdeep_runs/run_30_11_2018_t_16_04_31

#testing input files
#testing input files
sanity_check_reads_ready_file.pl reads_collapsed_prova.fa

started: 16:4:32
Error: problem with reads_collapsed_prova.fa
/usr/bin/env: "perl -W": File o directory non esistente
aga@THOR:~/Scrivania/SimoneF/mirdeep2-master/src$

[JulianC]

Yes I have that file. In fact the sanity check for it works well

[GenoMax]

Error: problem with reads_collapsed_prova.fa

Just to be sure is that file in proper format e.g. not empty, not corrupt, has the content the program expects.

[JulianC]

Ok, thank you. Have you ever faced with this kind of error? (/usr/bin/env: "perl -W": file or directory not found)