For more than a month I am trying many tools for finding DE miRNAs in fungi but error, error, error
online tools don't support fungi and local tools were mostly written in perl needed mirdeep2 algorithms
believe my failure is not because of my laziness, I tried whatever I could
although being too rude with a great expectation, please someone help me to install mirdeep via TeamViewer or whatever
I asked institute admin, he tried his best but my problem was not solved
thank you in advance
It is often helpful if you share the error message with the community.
actually each software with its own error but mostly saying miRDeep ERROR :: system args failed: 6400
I understood that an earlier installation was succesfull, but that (after trying to reinstall) nothing works anymore. You also installed your own perl interpreter if I remember correctly. Somewhere, when reinstalling, something probably got wrongly configured and causing your problems.
I would try to remove everything I installed (including perl and perl modules) and start over from the beginning. Because it used to work, right?
you all right, I ran on replicate for Aspergillus fumigatus successfully but in the second replicate (before re-installing) only mapper.pl worked and quantifier.pl did not (too weird). then I re-installed but this time even mapper.pl does not work anymore
In perl scripts you generally define which perl to use in the shebang line. Did you do that?
you mean in mirdeep2.pl script I should change #!/usr/bin/perl to another directory?
If you installed your own perl (if the default one on the cluster is not one you can use) then you would change that line to the path of where this new perl program is (e.g. /home/izadi/bin/perl).
I only downloaded perl-5.24.0 and unzipped in
in /usr/home/izadi/ there 2 perl folders; perl which is empty and perl 5/bin contains only cpanm
Perhaps you should download e.g. latest perl source, extract, actually read the README file, google everything that you don't understand, and only then proceed with your stuff.
I performed like so
tar -xzf perl-5.24.0.tar.gz
All tests successful. Elapsed: 1242 sec u=4.69 s=1.59 cu=230.89 cs=25.09 scripts=2248 tests=851140
now in /usr/data/nfs6/izadi/ a folder was created name perl that is empty but I noticed mirdeep2.pl in perl-5.24.0 folder, what should I do now?
Please don't try to install things that are not necessary. They are making your life difficult. Your system perl which is at 5.22 should be fine for miRDeep2.
Start with a fresh download of miRDeep2 code. Open the README in that folder. Start at section 2 in installation, since we know you can't get
perl install.plmethod to work. Follow each step sequentially (2.1, 2.2 etc) until you complete them all. It is natural that you are starting to feel desperate by now but trying to do this methodically is the only way.
ok thank you
but from previous post where you advised me to follow 2.1 Sample Installation, I did and each step with its own error stopped me from ranfold to all
anyway thank you
If you had an error at each step then you need to address those errors sequentially. Moving to step 2.2. is not going to make the problem with 2.1 go away magically. You may be able to skip some steps (e.g. if you have bowtie installed already then use that PATH and go to the next app).
I will try the steps again and ask help for each error in a new thread.
Followed the steps in miRDeep2 README section 2 to verify that everything is working as included (on linux mint). So you should be able to do it. You would need to install Font-TTF-1.05 package from CPAN for the PDF-API2 to work.
thank you for paying attention
fortunately admin installed Font-TTF package from fedora repository just yesterday.
sorry for the below instruction from example installation
**for attach the miRDeep2 executable path to your PATH
did I perform right?
[izadi@lbox200 mirdeep2_0_0_8]$ setenv PATH
[izadi@lbox200 mirdeep2_0_0_8]$ setenv PATH $PATH\:/usr/data/nfs6/izadi/mirdeep2_0_0_8/
That echo command won't be useful since you are not using bash shell.
You could do
to enter a new bash shell. The system prompt will return but you should now be in a new bash shell. Confirm by
That will make it easy to follow the instructions from README as is.
echo $PATHshow now?
[izadi@lbox200 mirdeep2_0_0_8]$ echo $PATH /usr/local/sparky/bin:/usr/local/moltemplate/src:/usr/local2/app/MathWorks/MATLAB:/usr/local2/app/Wolfram/Mathematica:/usr/local2/app/intel/Compiler/11.1/059/bin/intel64:/usr/local2/app/abaqus:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:.:/usr/local2/scripts:/usr/data/nfs6/izadi/mirdeep2_0_0_8/src/:/usr/data/nfs6/izadi/mirdeep2_0_0_8/:/usr/data/nfs6/izadi/bowtie-1.1.2/ [izadi@lbox200 mirdeep2_0_0_8]$
That look ok. So on to step 2.
in the next step this happened
[izadi@lbox200 ViennaRNA-2.2.10]$ configure --prefix=/usr/data/nfs6/izadi/mirdeep2_0_0_8/
checking for Perl dynamic library extension... .so
checking for perl... /usr/bin/perl
checking for perl module ExtUtils::Embed... no
configure: error: Require ExtUtils::Embed to proceed
then I performed so
tar xvzf ExtUtils-Embed-1.14.tar.gz
make make install
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/share/man/man3'
Do not have write permissions on '/usr/share/man/man3'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at -e line 1.
Makefile:694: recipe for target 'pure_perl_install' failed
make: * [pure_perl_install] Error 13
Same problem. You don't have root privileges so you can't write to /usr.
See if these instructions help in installing the modules "user space". They add another complication : http://blogs.perl.org/users/marc_sebastian_jakobs/2009/11/how-to-install-perl-modules-from-cpan-in-the-unix-user-space.html
BTW: I did not need to install ExtUtils but looks like you don't have them. Why are you using your mirdeep directory as prefix for ViennaRNA package. Use the directory for ViennaRNA.
thank you for your sincere effort to help me to solve my problem
in step 2 I got confused and could not figure out what to do
tomorrow I will start my trying from step 2
According to the README miRDeep2 can use any perl in 5.x series. So the system perl in your case should be fine. What does
[izadi@lbox200 bin]$ perl -version
This is perl 5, version 22, subversion 2 (v5.22.2) built for x86_64-linux-thread-multi
So you tried reinstalling, but without first removing everything? (It's not sure that that will work, but it might)
I tried to install mirdeep2 a few days ago to see whether I also had problems, but it went perfect and test data worked without issues.
I removed mirdep2 folder and unziped again but this time when running mapper.pl or wherever saying
[izadi@lbox200 bin]$ mapper.pl 1.fq -e -h -m -v -p af -s sample.fa -t Sample.arf
Please run the install.pl script first before using the miRDeep2 package
The install script is located in /usr/data/nfs6/izadi/mirdeep2_0_0_8/ so just do
and when I ran perl install.pl telling
Installing PDF-API2 now
randfold was/is not installed properly
bowtie was/is not installed properly
pdf was/is not installed properly
RNAfold was/is not installed properly
Please run the install.pl script again to check if
everything is properly installed.
like an infinite circle :( :(
Dear F, Hi
If you intend to use miEDeep and miRDeep2, you must have reference genome.
Do you have such genome for your "fungi" ?
yes I have from ensemble
So I did not get the point that what part of your new "post" has changed.
Is it a new "post" or you have just remove something from old one ?
sorry, Farbod I did not get what you mean and which post you mean
you have asked this question before, now I can not find the new part of it.
is it an unsolved old question or it is a new (which part is new) one ?
yes, Farbod I removed my email. although I can't run mirdeep2 yet :(
exactly, I was searching your email! ;-) of course it seems that contacting with email is forbidden and insecure here.
actually I think here is secure but I don't like my mentor knows I am solving my problems barely by biostars :(
might be she suddenly come across this post
So, your mentor wants you to install mirdeep2 correctly or to find DEGs of your fungi miRNAs?
no she only asked me via a good pipeline with detailed description give her DEGs table. but I only performed so by online tool which she did not accept :(