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  • nilshomer
    replied
    Add this line "fprintf(stderr, "errCode=%d\n", errCode);" in RunMatch.c. See the context (called a diff) above.

    My guess is that it is not BFAST related, but related to your specific operating system configuration. This would be a good time to talk to your system administrator and/or seek bioinformatics help.

    Leave a comment:


  • bsk8635
    replied
    Hi Nils,

    Please bear with me for a second. I am not familiar with C at all, so could you please tell me which file (I assume RunMatch.c) and exactly where in the file (line number might be helpful) I need to add the given lines of code? The version of bfast installed on the cluster is 0.6.5a.

    Thank you very much for your help with this issue.

    - Boryana

    Leave a comment:


  • nilshomer
    replied
    Report what the error code is. To do so, add the following to the code and re-compile:
    Code:
    diff --git a/bfast/RunMatch.c b/bfast/RunMatch.c
    index d8e7de3..3cffe1a 100644
    --- a/bfast/RunMatch.c
    +++ b/bfast/RunMatch.c
    @@ -853,6 +853,7 @@ int FindMatches(char **indexFileName,
                                            FindMatchesThread, /* start routine */
                                            &data[i]); /* data to routine */
                            if(0!=errCode) {
    +                            fprintf(stderr, "errCode=%d\n", errCode);
                                    PrintError(FnName, "pthread_create: errCode", "C
                            }
                    }

    Leave a comment:


  • bsk8635
    started a topic BFAST error durig match: Could not start thread

    BFAST error durig match: Could not start thread

    Hi,

    I have been playing around with BFAST the last couple of days and I can't get past the match step as it gives me the following error message after it has checked my command line arguments:


    $ bfast match -f MgIM62u.fasta -r A1.fastq > bfast.matches.MgIM62u.bmf
    ************************************************************
    Checking input parameters supplied by the user ...
    Validating fastaFileName MgIM62u.fasta.
    Validating readsFileName A1.fastq.
    Validating tmpDir path ./.
    **** Input arguments look good!
    ************************************************************
    ************************************************************
    Printing Program Parameters:
    programMode: [ExecuteProgram]
    fastaFileName: MgIM62u.fasta
    mainIndexes [Auto-recognizing]
    secondaryIndexes [Not Using]
    readsFileName: A1.fastq
    offsets: [Using All]
    loadAllIndexes: [Not Using]
    compression: [Not Using]
    space: [NT Space]
    startReadNum: 1
    endReadNum: 2147483647
    keySize: [Not Using]
    maxKeyMatches: 8
    maxNumMatches: 384
    whichStrand: [Both Strands]
    numThreads: 1
    queueLength: 250000
    tmpDir: ./
    timing: [Not Using]
    ************************************************************
    Searching for main indexes...
    Found 1 index (1 file).
    Not using secondary indexes.
    ************************************************************
    Reading in reference genome from MgIM62u.fasta.nt.brg.
    In total read 1546 contigs for a total of 313500235 bases
    ************************************************************
    Reading A1.fastq into a temp file.
    Will process 30325510 reads.
    ************************************************************
    Searching index file 1/1 (index #1, bin #1)...
    Reading index from MgIM62u.fasta.nt.1.1.bif.
    Read index from MgIM62u.fasta.nt.1.1.bif.
    Reads processed: 0************************************************************
    In function "FindMatches": Fatal Error[ThreadError]. Variable/Value: pthread_create: errCode.
    Message: Could not start thread.
    ***** Exiting due to errors *****
    ************************************************************


    Any ideas what this is related to? Since I have no idea what the problem is related to, I don't really know what additional information I should provide to help you help me.

    Thanks in advance for your help!

    -Boryana
    Last edited by bsk8635; 06-15-2011, 09:18 AM.
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