>>
>> I am trying to use your Ray assembler. I've been using Spades (mainly
>> because I am formerly
>> from Pavel Pevzner's lab) but running out of memory on a large dataset.
>
> Maybe processing your large dataset is more amenable with a distributed
> assembler.
Spades group released a new version yesterday that's supposed to use less
memory. I am trying that and the Ray assembler.
> To get it and install it:
>
> $ wget
> http://downloads.sourceforge.net/project/denovoassembler/Ray-v2.1.0.tar.bz2
> $ sha1sum Ray-v2.1.0.tar.bz2
> 4c09f2731445852857af53b65aa47e444792eeb0 Ray-v2.1.0.tar.bz2
>
> $ tar xjf Ray-v2.1.0.tar.bz2
> $ cd Ray-v2.1.0/
> $ make
The problem is this compilation error: After those steps I get the following
error:
eggs:~/Ray-v2.1.0$ make
Compilation options (you can change them of course)
PREFIX = install-prefix
MAXKMERLENGTH = 32
FORCE_PACKING = n
ASSERT = n
HAVE_LIBZ = n
HAVE_LIBBZ2 = n
INTEL_COMPILER = n
MPICXX = mpicxx
GPROF = n
OPTIMIZE = y
DEBUG = n
Compilation and linking flags (generated automatically)
CXXFLAGS = -Wall -std=c++98 -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.1.0\"
LDFLAGS =
make[1]: Entering directory `/s/parsons/f/fac/cboucher/Ray-v2.1.0/RayPlatform'
mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.1.0\" -D
RAYPLATFORM_VERSION=\"1.1.0\" -I. -c -o memory/ReusableMemoryStore.o
memory/ReusableMemoryStore.cpp
make[1]: mpicxx: Command not found
make[1]: *** [memory/ReusableMemoryStore.o] Error 127
make[1]: Leaving directory `/s/parsons/f/fac/cboucher/Ray-v2.1.0/RayPlatform'
make[1]: Entering directory `/s/parsons/f/fac/cboucher/Ray-v2.1.0/code'
mpicxx -Wall -std=c++98 -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.1.0\" -I
../RayPlatform -I. -c -o application_core/ray_main.o
application_core/ray_main.cpp
make[1]: mpicxx: Command not found
make[1]: *** [application_core/ray_main.o] Error 127
make[1]: Leaving directory `/s/parsons/f/fac/cboucher/Ray-v2.1.0/code'
mpicxx code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
make: mpicxx: Command not found
make: *** [Ray] Error 127
Any thoughts?
In addition, is the the max kmer length 32? Most people are using upwards to
55….?
Christina
>
> $ mpiexec -n 1 ./Ray -version
> $ mpiexec -n 999 ./Ray -k 31 -p 1.left.fastq 1.right.fastq -p 2.left.fastq
> 2.right.fastq -o Test
>
>> Best,
>> Christina
>>
>> *
>> ------------------------------------------------*
>> *Christina Boucher*
>> **Department of Computer Science
>> Colorado State University
>> Fort Collins, CO 80523
>> +1.970.491.8063
>> cbouc...@cs.colostate.edu <mailto:cbouc...@cs.colostate.edu>
>> www.christinaboucher.com <http://www.christinaboucher.com>
>> *------------------------------------------------*
>>
>
------------------------------------------------
Christina Boucher
Department of Computer Science
Colorado State University
Fort Collins, CO 80523
+1.970.491.8063
cbouc...@cs.colostate.edu
www.christinaboucher.com
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