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  • Mokhtar
    replied
    Please is there any one can help me how can I BLAST one FASTA file with more than 3000 sequences

    Leave a comment:


  • cherubzhen
    replied
    Hi Chip

    I am trying to run spanner. Would you able to help me? What is your email? Mine is [email protected]

    Thanks

    Originally posted by ChipStewart View Post
    Hi Yan,

    It has been a while since I worked on Spanner but I may be able to help.

    The first step should be to execute this command:

    Spanner --scan --infile <your Mosaik Alignment file> --outdir <scan directory>

    which should make a '*.stats file in output directory. The stats file is an ascii file listing fragment length distributions for each library in the bam file.

    There are three remaining steps after this. If you wish to proceed, perhaps it would be best to contact me directly.


    Thanks,

    Chip

    Leave a comment:


  • kksiame
    replied
    Spanner Compilation Error

    Dear Chip,
    I had trouble compiling Spanner. Find below details of the errors I got. I'm a bit of a novice and would appreciate any help from anyone.

    In file included from MosaikAlignment.cpp:12:
    MosaikAlignment.h:374: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h: In constructor ‘Mosaik::ReferenceSequence::ReferenceSequence()’:
    MosaikAlignment.h:387: error: class ‘Mosaik::ReferenceSequence’ does not have any field named ‘NumAligned’
    MosaikAlignment.h: At global scope:
    MosaikAlignment.h:411: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h:413: error: ‘uint64_t’ does not name a type
    In file included from MosaikAlignment.cpp:12:
    MosaikAlignment.h:447: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h:448: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h:450: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h:501: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h:503: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h:533: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h:534: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h:585: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h:588: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h:590: error: ‘uint64_t’ does not name a type
    MosaikAlignment.h:591: error: ‘uint64_t’ does not name a type
    MosaikAlignment.cpp: In constructor ‘Mosaik::CAlignmentReader::CAlignmentReader()’:
    MosaikAlignment.cpp:24: error: class ‘Mosaik::CAlignmentReader’ does not have any field named ‘mNumReads’
    MosaikAlignment.cpp:25: error: class ‘Mosaik::CAlignmentReader’ does not have any field named ‘mNumBases’
    MosaikAlignment.cpp:26: error: class ‘Mosaik::CAlignmentReader’ does not have any field named ‘mCurrentRead’
    MosaikAlignment.cpp: In static member function ‘static bool Mosaik::CAlignmentReader::CheckFile(const std::string&, bool)’:
    MosaikAlignment.cpp:64: error: ‘fopen’ was not declared in this scope
    MosaikAlignment.cpp:67: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp:78: error: ‘fread’ was not declared in this scope
    MosaikAlignment.cpp:80: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp:90: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp:100: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp:110: error: ‘fclose’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentReader::Close()’:
    MosaikAlignment.cpp:120: error: ‘fclose’ was not declared in this scope
    MosaikAlignment.cpp: At global scope:
    MosaikAlignment.cpp:129: error: ‘uint64_t’ does not name a type
    MosaikAlignment.cpp:135: error: ‘uint64_t’ does not name a type
    MosaikAlignment.cpp: In member function ‘Mosaik::ReadGroup Mosaik::CAlignmentReader::GetReadGroupFromCode(unsigned int)’:
    MosaikAlignment.cpp:145: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentReader::Jump(unsigned int, unsigned int)’:
    MosaikAlignment.cpp:179: error: ‘fseeko’ was not declared in this scope
    MosaikAlignment.cpp:183: error: ‘fread’ was not declared in this scope
    MosaikAlignment.cpp:225: error: ‘mCurrentRead’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘bool Mosaik::CAlignmentReader::LoadNextRead(Mosaik::AlignedRead&)’:
    MosaikAlignment.cpp:239: error: ‘mCurrentRead’ was not declared in this scope
    MosaikAlignment.cpp:239: error: ‘mNumReads’ was not declared in this scope
    MosaikAlignment.cpp:277: error: ‘mCurrentRead’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentReader::Open(const std::string&)’:
    MosaikAlignment.cpp:328: error: ‘fopen’ was not declared in this scope
    MosaikAlignment.cpp:356: error: ‘fseeko’ was not declared in this scope
    MosaikAlignment.cpp:359: error: ‘fgetc’ was not declared in this scope
    MosaikAlignment.cpp:362: error: ‘fread’ was not declared in this scope
    MosaikAlignment.cpp:375: error: ‘mNumReads’ was not declared in this scope
    MosaikAlignment.cpp:378: error: ‘mNumBases’ was not declared in this scope
    MosaikAlignment.cpp:456: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp:472: error: ‘ftello’ was not declared in this scope
    MosaikAlignment.cpp:516: error: ‘struct Mosaik::ReferenceSequence’ has no member named ‘NumAligned’
    MosaikAlignment.cpp:557: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘bool Mosaik::CAlignmentReader::ReadPartition()’:
    MosaikAlignment.cpp:752: error: ‘fread’ was not declared in this scope
    MosaikAlignment.cpp:754: error: ‘feof’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentReader::ReadTag(Mosaik::Tag&)’:
    MosaikAlignment.cpp:793: error: ‘fgetc’ was not declared in this scope
    MosaikAlignment.cpp:807: error: ‘fread’ was not declared in this scope
    MosaikAlignment.cpp:838: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentReader::Rewind()’:
    MosaikAlignment.cpp:845: error: ‘fseeko’ was not declared in this scope
    MosaikAlignment.cpp:846: error: ‘mCurrentRead’ was not declared in this scope
    MosaikAlignment.cpp: In constructor ‘Mosaik::CAlignmentWriter::CAlignmentWriter()’:
    MosaikAlignment.cpp:859: error: class ‘Mosaik::CAlignmentWriter’ does not have any field named ‘mNumReads’
    MosaikAlignment.cpp:860: error: class ‘Mosaik::CAlignmentWriter’ does not have any field named ‘mNumBases’
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentWriter::AddHeaderTag(const Mosaik::Tag&)’:
    MosaikAlignment.cpp:899: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentWriter::Close()’:
    MosaikAlignment.cpp:946: error: ‘ftello’ was not declared in this scope
    MosaikAlignment.cpp:971: error: ‘fputc’ was not declared in this scope
    MosaikAlignment.cpp:983: error: ‘fwrite’ was not declared in this scope
    MosaikAlignment.cpp:986: error: ‘const struct Mosaik::ReferenceSequence’ has no member named ‘NumAligned’
    MosaikAlignment.cpp:1024: error: ‘fwrite’ was not declared in this scope
    MosaikAlignment.cpp:1052: error: ‘fseeko’ was not declared in this scope
    MosaikAlignment.cpp:1053: error: ‘mNumReads’ was not declared in this scope
    MosaikAlignment.cpp:1053: error: ‘fwrite’ was not declared in this scope
    MosaikAlignment.cpp:1056: error: ‘mNumBases’ was not declared in this scope
    MosaikAlignment.cpp:1077: error: ‘fclose’ was not declared in this scope
    MosaikAlignment.cpp: At global scope:
    MosaikAlignment.cpp:1081: error: ‘uint64_t’ does not name a type
    MosaikAlignment.cpp:1086: error: ‘uint64_t’ does not name a type
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentWriter::Open(const std::string&, const std::vector<Mosaik::ReferenceSequence, std::allocator<Mosaik::ReferenceSequence> >&, const std::vector<Mosaik::ReadGroup, std::allocator<Mosaik::ReadGroup> >&, Mosaik::AlignmentStatus)’:
    MosaikAlignment.cpp:1100: error: ‘fopen’ was not declared in this scope
    MosaikAlignment.cpp:1124: error: ‘struct Mosaik::ReferenceSequence’ has no member named ‘NumAligned’
    MosaikAlignment.cpp:1163: error: ‘fwrite’ was not declared in this scope
    MosaikAlignment.cpp:1166: error: ‘fputc’ was not declared in this scope
    MosaikAlignment.cpp:1174: error: ‘uint64_t’ was not declared in this scope
    MosaikAlignment.cpp:1174: error: expected ‘;’ before ‘currentTime’
    MosaikAlignment.cpp:1175: error: ‘currentTime’ was not declared in this scope
    MosaikAlignment.cpp:1184: error: ‘fseeko’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentWriter::SaveAlignedRead(const Mosaik::AlignedRead&)’:
    MosaikAlignment.cpp:1290: error: ‘mNumReads’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentWriter::WriteAlignment(const Mosaik::Alignment*, bool, bool, bool, bool)’:
    MosaikAlignment.cpp:1308: error: ‘struct Mosaik::ReferenceSequence’ has no member named ‘NumAligned’
    MosaikAlignment.cpp:1413: error: ‘mNumBases’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentWriter::WritePartition()’:
    MosaikAlignment.cpp:1457: error: ‘ftello’ was not declared in this scope
    MosaikAlignment.cpp:1471: error: ‘fwrite’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CAlignmentWriter::WriteTag(const std::_Rb_tree_const_iterator<std:air<const unsigned char, Mosaik::Tag> >&)’:
    MosaikAlignment.cpp:1493: error: ‘fputc’ was not declared in this scope
    MosaikAlignment.cpp:1506: error: ‘fwrite’ was not declared in this scope
    MosaikAlignment.cpp:1538: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp: At global scope:
    MosaikAlignment.cpp:1583: error: ‘uint64_t’ does not name a type
    MosaikAlignment.cpp:1584: error: ‘uint64_t’ does not name a type
    MosaikAlignment.cpp:1588: error: ‘uint64_t’ does not name a type
    MosaikAlignment.cpp:1607: error: ‘uint64_t’ does not name a type
    MosaikAlignment.cpp: In constructor ‘Mosaik::CFastLZIO::CFastLZIO()’:
    MosaikAlignment.cpp:1624: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CFastLZIO::Read(char*&, unsigned int&, FILE*)’:
    MosaikAlignment.cpp:1648: error: ‘fread’ was not declared in this scope
    MosaikAlignment.cpp:1657: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CFastLZIO::Read(std::string&, FILE*)’:
    MosaikAlignment.cpp:1691: error: ‘fread’ was not declared in this scope
    MosaikAlignment.cpp: In member function ‘void Mosaik::CFastLZIO::Write(const char*, unsigned int, FILE*)’:
    MosaikAlignment.cpp:1721: error: ‘fwrite’ was not declared in this scope
    MosaikAlignment.cpp: In static member function ‘static unsigned int Mosaik::CSHA1::GenerateReadGroupCode(const std::string&, const std::string&)’:
    MosaikAlignment.cpp:1756: error: ‘sprintf’ was not declared in this scope
    MosaikAlignment.cpp: In static member function ‘static void Mosaik::CSequenceUtilities::Pack(std::string&, const std::string&, const std::string&)’:
    MosaikAlignment.cpp:2011: error: ‘printf’ was not declared in this scope
    MosaikAlignment.cpp:2025: warning: array subscript has type ‘char’
    MosaikAlignment.cpp:2025: warning: array subscript has type ‘char’
    make: *** [MosaikAlignment.o] Error 1
    Last edited by kksiame; 04-02-2013, 06:02 AM.

    Leave a comment:


  • pengyanbenben
    replied
    Hi Chip,

    I just read this message! Thanks very much for you reply!
    I executed the command you list and a '*.stat' file is generated. Could you told me how to do in the following steps?

    If possible, you can send me email(pengyanbenben@live,cn).

    Thanks again for your help!!

    Yan

    Leave a comment:


  • ChipStewart
    replied
    Hi Yan,

    It has been a while since I worked on Spanner but I may be able to help.

    The first step should be to execute this command:

    Spanner --scan --infile <your Mosaik Alignment file> --outdir <scan directory>

    which should make a '*.stats file in output directory. The stats file is an ascii file listing fragment length distributions for each library in the bam file.

    There are three remaining steps after this. If you wish to proceed, perhaps it would be best to contact me directly.


    Thanks,

    Chip

    Leave a comment:


  • ekg
    replied
    Just to be clear, the current focus of Tangram is mobile element insertions. CNV detection is a future development.

    Leave a comment:


  • ekg
    replied
    The new MEI detector is called Tangram, and it has been released under an MIT license: https://github.com/jiantao/Tangram!

    Please inform the author, Jiantao Wu, if you encounter any issues in using the detector.

    Leave a comment:


  • ekg
    replied
    I'm in Chip's old Lab (Gabor Marth's group). A member of our group has developed a new mobile element insertion detector. It's performing well in tests but I'm not sure if it's ready for public use. It should be relatively soon.

    It requires mapping using the most recent version of MOSAIK, which is designed to deliver information about multiple mappings. The user must also map against a reference which includes the mobile elements of interest.

    If you are interested in using this detection method, I would suggest you email me (erik dot garrison at bc dot edu) and I will put you in touch with the developer.

    Leave a comment:


  • pengyanbenben
    replied
    Hi,

    Do you have any idea about how to use Spanner?? I can sucessfully compile the source code and generate the binary "Spanner". However, there is an error when running the data:

    begin Spanner! Version 6.30
    command line:
    ./Spanner -i read_A13.mka.sorted.bam
    @RG ID:A13_ID LB:A13_library PI:300 PL:illumina PU:A13 SM: Daphnia_A13
    Number of Libraries: 1
    Segmentation fault (core dumped)

    I don't know what's going on and what should I do to solve the problem?

    I'll appreciate if anyone can provide help!

    Yan

    Leave a comment:


  • Margarida
    replied
    Thank you. That's really helpful.

    Leave a comment:


  • Zam
    replied
    Chip Stewart developed it, at Boston College. He's moved to somewhere else now - the Broad?

    Leave a comment:


  • Margarida
    started a topic SPANNER (1000 genomes)

    SPANNER (1000 genomes)

    Hello everyone,

    SPANNER is a CNV caller that performed quite well in the 1000 genomes project. I would really like to see how it performs on my genomic data but I cannot find information anywhere about this program (much less where to download it) with the exception of the supplementary materials of the 1000 genomes paper.

    Does anyone know who develop (is developing) SPANNER and when will it be available to the whole community? It looks like it will be a great addition to the CNV field.

    Thanks!!

    Margarida

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