CEGMA Errors

cegma.stderr

$ cegma --genome sample.dna --protein sample.prot -o sample -v --ext --tmp
Duplicate specification "T|threads=i" for option "t"


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

RUNNING: genome_map  -n genome -p 6 -o 5000 -c 2000 -t 1  -v  sample.prot sample.dna 2>sample.cegma.errors


Building a new DB, current time: 08/18/2011 10:37:59
New DB name:   /tmp/genome19064.blastdb
New DB title:  sample.dna
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Adding sequences from FASTA; added 1 sequences in 0.178055 seconds.
Processing KOG: KOG0292 
Processing KOG: KOG0328 
Processing KOG: KOG0466 
Processing KOG: KOG0631 
Processing KOG: KOG0659 
Processing KOG: KOG1458 
Processing KOG: KOG1742 
Processing KOG: KOG1762 
Processing KOG: KOG1769 
Processing KOG: KOG1780 
Processing KOG: KOG1992 
Processing KOG: KOG2067 
Processing KOG: KOG2803 
Processing KOG: KOG2916 
Processing KOG: KOG3180 
Processing KOG: KOG3232 
Processing KOG: KOG3418 
Processing KOG: KOG3497 
Found 86 candidate regions in sample.dna


********************************************************************************
**     MAKING INITIAL GENE PREDICTIONS FOR CORE GENES (GENEWISE + GENEID)     **
********************************************************************************

RUNNING: local_map -n local -f -h /home/rob/src/cegma/current/data/hmm_profiles -i KOG -v  genome.chunks.fa 2>sample.cegma.errors
Processing chunk: KOG0292.1
Processing chunk: KOG0292.6
FATAL ERROR! 6400: "No such file or directory"

sample.cegma.errors

Warning Error
	Major problem (!) - in GeneLoop6 matrix to special read off, position
0,0 state 0 no source found!
Warning Error
	In GeneLoop6 read off ending at 0 ... got a bad matrix to special
read off... returning partial alignment
Can't use an undefined value as an ARRAY reference at /home/rob/src/cegma/current/bin/parsewise line 217.
Can't run parsewise

Hello, I am also getting the same error message,, did you find any solution to fix this error ??

The probably suspect is an incorrect version of glib. For some bizarre reason, you need an ancient version of glib for cegma to work. Do you know which version of glib you have?

I have got the same question and with glib 2.0

-bash-3.2$ locate libglib
/lib/libglib-2.0.so.0
/lib/libglib-2.0.so.0.1200.3
/lib64/libglib-2.0.a
/lib64/libglib-2.0.so
/lib64/libglib-2.0.so.0
/lib64/libglib-2.0.so.0.1200.3

Perhaps try the new.instructions up.at http://korflab.ucdavis.edu/Datasets/cegma/ubuntu_instructions_1.txt or http://korflab.ucdavis.edu/Datasets/cegma/ubuntu_instructions_2.txt