# assuming /path/to/CEGMA represents a valid path to your local CEGMA installation:

% cegma -g /path/to/CEGMA/sample/sample.dna -p /path/to/CEGMA/sample/sample.prot



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

RUNNING: genome_map  -n genome -p 6 -o 5000 -c 2000 -t 16  /path/to/CEGMA/sample/sample.prot /path/to/CEGMA/sample/sample.dna 2>output.cegma.errors


Building a new DB, current time: 04/30/2012 11:42:26
New DB name:   /tmp/genome86278.blastdb
New DB title:  /path/to/CEGMA/sample/sample.dna
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Adding sequences from FASTA; added 1 sequences in 0.0646069 seconds.
Found 86 candidate regions in /path/to/CEGMA/sample/sample.dna


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

RUNNING: local_map -n local -f -h /path/to/CEGMA/data/hmm_profiles -i KOG  genome.chunks.fa 2>output.cegma.errors
NOTE: created 23 geneid predictions


********************************************************************************
**           FILTERING INITIAL PROTEINS PRODUCED BY GENEID (HMMER)            **
********************************************************************************

RUNNING: hmm_select -i KOG -o local -t 16  /path/to/CEGMA/data/hmm_profiles local.geneid.fa /path/to/CEGMA/data/profiles_cutoff.tbl 2>output.cegma.errors
NOTE: Found 15 geneid predictions with scores above threshold value


********************************************************************************
**       CALCULATING GENEID PARAMETERS FROM SELECTED GENEID PREDICTIONS       **
********************************************************************************

RUNNING: geneid-train  local.geneid.selected.gff local.geneid.selected.dna geneid_params 2>output.cegma.errors
DATA COLLECTED: 15 Coding sequences containing 48 introns 
RUNNING: make_paramfile /path/to/CEGMA/data/self.param.template \
	    geneid_params/coding.initial.5.logs geneid_params/coding.transition.5.logs \
	    geneid_params/start.logs geneid_params/acc.logs geneid_params/don.logs \
	    geneid_params/intron.max >  geneid_params/self.param


********************************************************************************
**                           ACCURATE LOCAL MAPPING                           **
********************************************************************************

RUNNING: local_map -n local_self -g local.genewise.gff -d geneid_params/self.param -h /path/to/CEGMA/data/hmm_profiles -i KOG  genome.chunks.fa 2>output.cegma.errors
NOTE: Will use specifed local.genewise.gff file instead of running genewise
NOTE: created 21 geneid predictions


********************************************************************************
**                              FINAL FILTERING                               **
********************************************************************************

RUNNING: hmm_select -i KOG -o local_self -t 16  /path/to/CEGMA/data/hmm_profiles local_self.geneid.fa /path/to/CEGMA/data/profiles_cutoff.tbl 2>output.cegma.errors
NOTE: Foud 15 geneid predictions with scores above threshold value


********************************************************************************
**         CONVERTING LOCAL COORDINATES INTO GENOME-WIDE COORDINATES          **
********************************************************************************



********************************************************************************
**    EVALUATING RESULTS AND COMPARING TO SET OF 248 HIGHLY CONSERVED CEGS    **
********************************************************************************

RUNNING: completeness  local_self.hmm_select.aln /path/to/CEGMA/data/completeness_cutoff.tbl > output.completeness_report





# if this all has worked correctly, you should see the following file sizes

% ls -l

total 272
-rw-r--r--  1 keith  staff  99177 May 14 09:49 output.cegma.dna
-rw-r--r--  1 keith  staff      0 May 14 09:49 output.cegma.errors
-rw-r--r--  1 keith  staff   5484 May 14 09:49 output.cegma.fa
-rw-r--r--  1 keith  staff   8325 May 14 09:49 output.cegma.gff
-rw-r--r--  1 keith  staff    155 May 14 09:49 output.cegma.id
-rw-r--r--  1 keith  staff   8075 May 14 09:49 output.cegma.local.gff
-rw-r--r--  1 keith  staff   1330 May 14 09:49 output.completeness_report