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yuwwu / ezTree

A Perl pipeline for identifying marker genes and build phylogenetic trees for a set of genomes
GNU General Public License v3.0
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Sample test tutorial fails to open fasta file #1

Open cirodri1 opened 6 years ago

cirodri1 commented 6 years ago

Dear all,

When I was trying to go over the tutorial I ran into a problem when trying the command: ./ezTree -list list_species -out list_species.out

It downloads the PFAM database as shown here:

screen shot 2018-05-02 at 10 54 44 am

but then it gives me a message saying "Cannot open sequence file Escherichia_coli_E24377A.fasta" Even though the file is inside the folder:

screen shot 2018-05-02 at 10 55 57 am

Does anyone have any clue on how to solve this?

Thanks for your help!

Lolita05 commented 6 years ago

Hello!

I have the same problem. Do you find the solution?

thanks in advance for the answer!

mpunzalan commented 5 years ago

Hi @cirodri1,

The list_species file must be in the same directory as the fasta files. Therefore, you must be inside the test_example directory and run the ff:

../ezTree -list list_species -out list_species.out

I noticed that ezTree cannot open the sequence file if you are not inside the directory of the sequence files. Example:

(inside the ezTree directory) ./ezTree -list test_example/list_species -out test_example/list_species.out

^this will give the same error as yours.