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Old 01-04-2016, 05:09 AM   #1
voidnyx
Junior Member
 
Location: Germany

Join Date: Jun 2015
Posts: 7
Default CEGMA Error genome_map 6400

Hi,

I am trying to get CEGMA to run on our cluster. After the horrors of genewise installation I thought i had everything complete but now I recieve:


********************************************************************************
** 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>../test_run/sample.cegma.errors


Building a new DB, current time: 01/04/2016 14:59:37
New DB name: /tmp/genome13761.blastdb
New DB title: ../sample/sample.dna
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 1 sequences in 0.065515 seconds.
FATAL ERROR when running genome_map 6400: ""


Ending CEGMA


when I try to run CEGMA with: /project/molgen/Bio/CEGMA_v2.5/bin$ ./cegma --genome ../sample/sample.dna --protein ../sample/sample.prot -o ../test_run/sample


I have installed genewise (wise2.4.1), geneid (1.4.4) and hmmer (3.1b2 and also tried 3.0).

I have them all added to my path:

/project/molgen/Bio/hmmer-3.0/src/:
/project/molgen/Bio/geneid_1.4.4/bin/:
/project/molgen/Bio/hmmer-3.1b2/bin/:
/project/molgen/Bio/wise2.4.1/src/bin/:
...

I can run them all from my terminal (tblastn also). And they all produce no Errors.

I can run cegma -h and it works fine.

But when I try to run cegma with the sample data set I get Error 6400.

I googled/searched and it seems 6400 indicates some missing dependency but I have no idea whats missing.


cat sample.cegma.errors gives me:

BLAST query/options error: Compressed alphabet lookup table requires word size 6 or 7
Please refer to the BLAST+ user manual.
Can't run tblastn


So is cegma using wrong parameters for tblastn?

Can anybody help?

Last edited by voidnyx; 01-04-2016 at 05:12 AM.
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Old 01-06-2016, 12:33 AM   #2
voidnyx
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Location: Germany

Join Date: Jun 2015
Posts: 7
Default

I managed to get it working.

Just in case someone stumbles across the same problem:

Turns out I had only exported the Variables CEGMA and CEGMATMP once by hand and not added to my bashrc so they were gone when I restarted.
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