Problem running CEGMA

[starbug16]

Hi,

I have installed the following as prerequisites for CEGMA version 2.4:

hmmer-3.0
geneid v1.4
genewise 2.4.1

While each program seems to run as it should individually, when I come to run the cegma command for the sample dataset I get the following output:


>cegma -g ../../sample/sample.dna -p ../../sample/sample.prot


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

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


Building a new DB, current time: 10/08/2014 11:49:11
New DB name: /tmp/genome7276.blastdb
New DB title: ../../sample/sample.dna
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Adding sequences from FASTA; added 1 sequences in 0.0435948 seconds.
Found 86 candidate regions in ../../sample/sample.dna


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

RUNNING: local_map -n local -f -h /home/tory/bin/cegma_v2.4.010312/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 1 /home/tory/bin/cegma_v2.4.010312/data/hmm_profiles local.geneid.fa /home/tory/bin/cegma_v2.4.010312/data/profiles_cutoff.tbl 2>output.cegma.errors
NOTE: Found 0 geneid predictions with scores above threshold value

The error file says:

local.geneid.selected.gff file does not exist

I can see that the local.geneid.gff files are created but not a selected file.

Does anyone have any ideas where I should start looking to debug this and what the correct output for the sample data should look like? I am guessing this is a problem with my hmmer output but could be wrong!

All help much appreciated!!

Tory

[kbradnam]

CEGMA sort of assumes that your genome assembly will be complete enough to have at least one core gene. When that doesn't happen you will see strange error messages. The clue in your output is:

"NOTE: Found 0 geneid predictions with scores above threshold value"

CEGMA still had one more step to run, which would have filtered down the current set of genes it had found. But at this stage you have no core genes in your assembly.

Regards,

Keith

[starbug16]

Ah, I probably should have mentioned this was running on the sample data which is why I assumed that there were core genes. I can't seem to replicate the sample output though...

Any help much appreciated,

Tory

[Sarry]

I had the same problem, just sort it out

Hi,

I had the same problem.
In my case, the actual hmmer version was not 3.0 but 2.3.2 (though I thought I checked before starting).
I recommend you double check your hmmer version with
>hmmsearch -h

If it did say an older version, make a path to correct one.

bests,

Sarry

[darked89]

CEGMA in Docker

There is a Docker container for CEGMA:

https://registry.hub.docker.com/u/robsyme/cegma-docker/

So instead of installing each component on its own one can just install Docker, execute few commands and have usable CEGMA. I think it may be easier than trying to resolve installation of several programs, sometimes with different versions on multiple platforms.

Hope it helps,

Darek