Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Cegma Error zgayk Bioinformatics 1 04-24-2015 07:08 AM
cegma genome_map error lilicano De novo discovery 0 02-11-2015 02:50 PM
CEGMA error flobpf Bioinformatics 12 01-27-2015 05:54 AM
CEGMA - FATAL ERROR when running local map 6400 reema Bioinformatics 7 09-15-2014 12:19 AM
CEGMA error condomitti Bioinformatics 12 05-07-2014 04:41 AM

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

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


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:


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:


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.
voidnyx is offline   Reply With Quote
Old 01-06-2016, 12:33 AM   #2
Junior Member
Location: Germany

Join Date: Jun 2015
Posts: 7

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.
voidnyx is offline   Reply With Quote

cegma, error

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:45 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO