CABOG: how to merge two genomes?

stvos · 01-13-2015, 08:47 AM

I want to merge two assemblies with Cabog 8.2, since Cabog can handle long fragments.

This is my command line:

module load cabog/x86_64/8.2
module load openmpi/x86_64/1.4.3
module list

runCA -d merged_assembly -p Artemia_inbred_merged -s CabogSpecfile_default.txt -version genome1.frg genome2.frg

I left the CabogSpecfile_default.txt completely default and just added the file names in the bottom of the specfile.

This is the error output I get:

Currently Loaded Modulefiles:

1) /perl/x86_64/5.14.1 3) /openmpi/x86_64/1.4.3
2) /gridengine/x86_64/2011.11 4) /cabog/x86_64/8.2
ENV: SGE_TASK_ID needs to be unset, done.
CA version 8.2 ($Id: AS_GKP_main.C 4535 2014-06-10 22:08:29Z skoren $).
CA version 8.2 ($Id: AS_CGB_unitigger.C 4518 2014-03-31 20:11:04Z brianwalenz $).
CA version 8.2 ($Id: BuildUnitigs.C 4371 2013-08-01 17:19:47Z brianwalenz $).
Using up to 64 OpenMP threads.
CA version 8.2 ($Id: AS_CGW_main.C 4557 2014-08-11 12:24:27Z brianwalenz $).
CA version 8.2 ($Id: terminator.C 4371 2013-08-01 17:19:47Z brianwalenz $).

Does anyone know what is the problem? I am also not getting any data output.

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01-13-2015, 08:47 AM	#1
stvos Junior Member Location: Belgium Join Date: Aug 2011 Posts: 7	CABOG: how to merge two genomes? I want to merge two assemblies with Cabog 8.2, since Cabog can handle long fragments. This is my command line: module load cabog/x86_64/8.2 module load openmpi/x86_64/1.4.3 module list runCA -d merged_assembly -p Artemia_inbred_merged -s CabogSpecfile_default.txt -version genome1.frg genome2.frg I left the CabogSpecfile_default.txt completely default and just added the file names in the bottom of the specfile. This is the error output I get: Currently Loaded Modulefiles: 1) /perl/x86_64/5.14.1 3) /openmpi/x86_64/1.4.3 2) /gridengine/x86_64/2011.11 4) /cabog/x86_64/8.2 ENV: SGE_TASK_ID needs to be unset, done. CA version 8.2 ($Id: AS_GKP_main.C 4535 2014-06-10 22:08:29Z skoren $). CA version 8.2 ($Id: AS_CGB_unitigger.C 4518 2014-03-31 20:11:04Z brianwalenz $). CA version 8.2 ($Id: BuildUnitigs.C 4371 2013-08-01 17:19:47Z brianwalenz $). Using up to 64 OpenMP threads. CA version 8.2 ($Id: AS_CGW_main.C 4557 2014-08-11 12:24:27Z brianwalenz $). CA version 8.2 ($Id: terminator.C 4371 2013-08-01 17:19:47Z brianwalenz $). Does anyone know what is the problem? I am also not getting any data output.