Unable to find lastz at AliTV.pm line 99.

[AllisonStander]

Good day,

I am having trouble running AliTV.

When I run alitv.pl on two fasta files, I get the following:

You are using version v1.0.6.
INFO - Wrote temporary YAML file 'test.yml'
INFO - Sequence names contain non-word-characters and will be replaced by unique sequence names. Failing sequence names are: '514776+,514184+,514064-,514704+,514064-,514782+,514788-,514782-,514064+,514704-,514064+,514184-(circular)', 'NC_003119.8'

FATAL - Unable to find lastz at /home/allison/Downloads/AliTV-perl-interface/bin/../lib/AliTV.pm line 99.

Unable to find lastz at /home/allison/Downloads/AliTV-perl-interface/bin/../lib/AliTV.pm line 99.

lastz is located at /home/allison/Downloads/lastz-distrib-1.04.03

I am unsure how to edit the AliTV.pm file, could you please assist? line 99 is the following: $aln_obj->run($self->_generate_seq_set());

Kind regards, Allison

[iimog]

Hi Allison,

alitv.pl assumes lastz to be available in the PATH. So you can add the folder with lastz (temporarily) to your PATH by executing this command before you run your alitv.pl command in the same shell:

export PATH=$PATH:/home/allison/Downloads/lastz-distrib-1.04.03

this assumes that the executable file called lastz is in that folder. You can permanently add this PATH by adding this line to your .bashrc or you could copy lastz to a location that is already on your PATH

As far as I know there is no way to configure the location of lastz using the config. @greatfireball tell me if I'm wrong.

Hope that helps! Let me know if you still have problems. Best regards, Markus

[greatfireball]

Hey Allison,

I wrote more or less the same answer as Markus did... Therefore, I think it should work in case you run it with lastz being available via PATH variable.

Best, Frank

[AllisonStander]

Thank you very much for the quick response.

I did: export PATH=$PATH:/home/allison/Downloads/lastz-distrib-1.04.03/bin before running alitv.pl and it ran successfully.

[iimog]

Awesome!

[ramadatta]

Thanks. Even after having lastz in the path did not fix the error for me.

I had to run the following command inside /AliTV/AliTV-perl-interface folder as mentioned here: https://github.com/AliTVTeam/AliTV-perl-interface/issues/149

$ cpanm --installdeps .

I also deleted old yaml file. It now works! :)