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 |
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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