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Interesting. This certainly is not happening for most people.
Could you go to the bug reporting site and describe the error there:
Please include any program output and command-line parameters as well.
The best chance for me to fix the bug you are experiencing is if I can reproduce the error in question.
Thanks for testing the software!
// Michael
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Firstly, thanks for making Mosaik available.
I have been trying the OS X build under OS X 10.4 ("Tiger") I too experienced segmentation faults (and bus errors) when running all Mosaik components. I managed to get them to run by compiling from source with the following modified macosx.inc
Code:# define our processor specific flags export PLATFORM_FLAGS = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Dstat64=stat -Dfstat64=fstat export LDFLAGS = -Wl
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@Nick: Thanks for the updated Mac OS X compilation options. These will be used when the MOSAIK update is pushed out this weekend.
@csffq: I'll take a look at why MOSAIK didn't like the '+' and '-' characters in the reference sequence names. Theoretically, it shouldn't matter, but I'll look into it either way.
Thanks again for the feedback,
// Michael
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How can make gigaBayes a little fast?
Currently I am using mosaic package to align my solexa reads to reference of transcriptome. It works well as producing snp and coverage information.
Here I write to ask for help as some problems happen to me. When I used mosaikassemble to produce assemble files, it produce more than ten thousands files because the reference is more than 20000 contigs. When I tried to use gigabayes to get snp information from those .gig files produced by mosaikassemble, I have to run the command one by one, it really costs a lot of time.
Is there any way to get only one resulting file from mosaikassemble command, so that I could run gigabayes only once to get all the snp information from transcriptome?
Or is there some way to ran gigabayes with those more than ten thousand files just faster?
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Re: about gigaBayes
I have merged the 20000 contigs into one whole sequence as you have said. with MosaikAssemble it produce only one .gig file. When using gigaBayes it still runs slowly, probably need 4-5 whole days to finish the task.
Fortunately I can just wait for the computer to finish the job, and then with perl scirpt to extract the useful information, thank you a lot!
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