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  • shahid.manzoor
    replied
    Hi all I want to use Mosaik for assembling a bacterial genome but the problem is that I can't access the API because when I go c++ or perl directory and write make it's gives error so any one can guide me about this, thanks in advance.

    Leave a comment:


  • csffq
    replied
    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!

    Leave a comment:


  • MattB
    replied
    cssffq, how about joining your contigs into a single 'reference'? You will know the contig boundaries, and can 'separate' them after. Could add some N's in between each contig to to make it easier to identify the boundaries.

    Leave a comment:


  • csffq
    replied
    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?

    Leave a comment:


  • snownebula
    replied
    @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

    Leave a comment:


  • csffq
    replied
    re:

    It seems the name of my contigs is not proper which cause the problem "segmentation fault". the name of the last hundreds of contigs have "+" and "-", as I deleted these, they work fine. thank you!

    Leave a comment:


  • Nick Miller
    replied
    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
    I haven't tested the output of the recompiled binaries extensively and I'm not a programmer so I don't know if the above changes will affect the results obtained with Mosaik.

    Leave a comment:


  • snownebula
    replied
    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

    Leave a comment:


  • csffq
    replied
    can not align now

    I cannot use the new versions 1.0

    The old version worked fine. When I change to use the new version. The step “mosaikaligner” tells“segmentation fault” although I have rebuilt the reference and reads.

    Leave a comment:


  • snownebula
    started a topic New version of MOSAIK available

    New version of MOSAIK available

    Hi guys,

    Just wanted to mention that a new version of MOSAIK is now available:



    Additionally, MOSAIK has finally been released under the GPL license! Feel free to grab the source here:



    Cheers,

    // Michael

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