Cegma Error

[zgayk]

Hello,

I realize there has been a whole discussion about this, but I have been trying to use cegma and encountered similar problems to others. Here is the error message I got:

********************************************************************************
** MAPPING PROTEINS TO GENOME (TBLASTN) **
********************************************************************************

RUNNING: genome_map -n genome -p 6 -o 5000 -c 2000 -t 1 /Users/macuser/Desktop/BBMAP//data/kogs.fa /Users/macuser/Desktop/BBMAP/Gaviaimmerheader.fasta 2>output.cegma.errors
FATAL ERROR when running genome_map 32512: ""

Here is the code I used:cegma -g Users/macuser/Desktop/BBMAP/Gaviaimmerheader.fasta -o /Users/macuser/Desktop/BBMAP/Gavia_immer.fasta

and the output.cegma.errors file gave this message: h: ./genome_map: No such file or directory


I know this has been discussed already, but I was wondering if there is any consensus on what exactly this error message means. Previous answers have suggested that this may mean one of cegma's dependencies is not installed, cegma can't find your file, or perhaps there is an error in your fasta file. Or can it mean any of these things in different situations?

I installed cegma simply by using homebrew and all of the dependences are listed . There are no pipe characters in my fasta headers. I am assuming that the problem is with finding the file as indicated by the output.cegma.error file. But since I gave the full path, I am not sure why this is (could this be because homebrew installs to /usr/local/Cellar and my files are on the desktop?). I have very limited bioinformatics experience so if anyone has any suggestions, I would be most appreciative of your advice.

Sincerely,
Zach

[kbradnam]

Sounds like your Unix PATH variable isn't being set correctly. Your system can't find genome_map…this is not a CEGMA error per se.

Where did you install the CEGMA binaries and what do you seen when you type:

echo $PATH
which genome_map