Created
August 18, 2011 02:43
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CEGMA Errors
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$ 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" |
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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 |
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
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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?