Provlems running VelvetOptimiser

[RodrigoZG]

Hi everyone,

When trying to run VelvetOptimiser.pl from the VelvetOptimiser-master directory, (downloaded from: https://github.com/tseemann/VelvetOptimiser ), I get the following error:

:~/Documents/VelvetOptimiser-master$ perl VelvetOptimiser.pl -h
This Perl not built to support threads
Compilation failed in require at VelvetOptimiser.pl line 35.
BEGIN failed--compilation aborted at VelvetOptimiser.pl line 35.

Any help would be greatly appreciated
Rodrigo

[neavemj]

What version of perl are you running?

I have VelvetOptimiser.pl working fine with perl 5.24.0. You also need to configure perl to allow thread usage at compile time.

[RodrigoZG]

Hi neavemj,

SOLVED: (placing updates here for any noobies like me that might be going through the same issue.

In the end, correctly installing BioPerl, using homebrew to download the expat library, then placing the VelvetOptimiser directory in the velvet directory (with velveth inside) solved the issues.

good luck to anyone with these problems.

Thank you again, neavemj


------------------------------------

I've managed to make some progress!

~/Documents/VelvetOptimiser-master# perl5.26.0 VelvetOptimiser.pl -h

****************************************************
VelvetOptimiser.pl Version 2.2.5
****************************************************
Number of CPUs available: 4
Current free RAM: 40.637GB
Can't exec "velveth": No such file or directory at /home/vagrant/Documents/VelvetOptimiser-master/VelvetOpt/hwrap.pm line 218.
Unable to find velveth, please ensure that the velvet executables are in your PATH.


-------------------------------------------------

Thank you for your help. I was trying to run it using running v5.20.1. I've updated to the most recent version: perl5.26.0, and selected thread usage at compile time, but get the following when I try to run it:

~/Documents/VelvetOptimiser-master$ perl5.26.0 VelvetOptimiser.pl -h
Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /home/vagrant/Documents/VelvetOptimiser-master /usr/local/lib/perl5/site_perl/5.26.0/x86_64-linux-thread-multi /usr/local/lib/perl5/site_perl/5.26.0 /usr/local/lib/perl5/5.26.0/x86_64-linux-thread-multi /usr/local/lib/perl5/5.26.0) at /home/vagrant/Documents/VelvetOptimiser-master/VelvetOpt/Assembly.pm line 238.
BEGIN failed--compilation aborted at /home/vagrant/Documents/VelvetOptimiser-master/VelvetOpt/Assembly.pm line 238.
Compilation failed in require at VelvetOptimiser.pl line 37.
BEGIN failed--compilation aborted at VelvetOptimiser.pl line 37.


Thank you for your help, I've only just begun to learn the bioinformatics basics. Do you think this is a problem with the BioPerl installation?

I haven't been able to find any helpful posts online on how to install the Bio::SeqIO module though...

[neavemj]

Nice work Rodrigo, looks like you've solved that first problem.

Yep, now you need to get BioPerl installed. You can check out their website for installation instructions (http://bioperl.org/INSTALL.html).

They have a few different recommendations on there. I'd personally try the simplest bit first, by typing:

cpan

Then find the name of the latest BioPerl package:

cpan>d /bioperl/

....

Distribution C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
Distribution C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
Distribution C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz

And install the most recent:

cpan>install C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz

If this doesn't work you might have to go back and follow the more detailed instructions.

Good luck!

Matt.

[RodrigoZG]

Thanks Matt,

All sorted now

[neavemj]

Sounds great Rodrigo!