Hello,
> make[1]: mpicxx: Command not found
To install Ray, you need an MPI library. You don't have one installed.
For example, on Fedora, the packages are openmpi, openmpi-devel, gcc-c++.
> In addition, is the the max kmer length 32? Most people are using upwards to
> 55….?
The maximum k-mer length is set at compilation. The default is MAXKMERLENGTH=32.
To change that:
make MAXKMERLENGTH=64
Sébastien
On 10/31/2012 12:50 PM, Christina Boucher wrote:
>>>
>>> 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
>>> [email protected] <mailto:[email protected]>
>>> <mailto:[email protected]>
>>> www.christinaboucher.com <http://www.christinaboucher.com>
>>> <http://www.christinaboucher.com>
>>> *------------------------------------------------*
>>>
>>
>
> *
> ------------------------------------------------*
> *Christina Boucher*
> **Department of Computer Science
> Colorado State University
> Fort Collins, CO 80523
> +1.970.491.8063
> [email protected] <mailto:[email protected]>
> www.christinaboucher.com <http://www.christinaboucher.com>
> *------------------------------------------------*
>
--
***
Sébastien Boisvert
http://boisvert.info
Sent from a PC (Linux panic 3.6.2-4.fc17.x86_64).
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