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  • vinay052003
    Member
    • Jan 2010
    • 59
    #1

    Empty junction.bed TopHat

    I ran TopHat on Gm12878 cell line RNA-Seq data (fastq files) from ENCODE project. The run was successful (no errors) but my junction.bed and insertion/deletion bed files are empty.
    My log/long_spanning_reads.log reports an error:

    dyld: lazy symbol binding failed: Symbol not found: __ZNSt8__detail15_List_node_base7_M_hookEPS0_
    Referenced from: /Users/vmittal3/usr/local/bin/long_spanning_reads
    Expected in: /usr/lib/libstdc++.6.dylib

    dyld: Symbol not found: __ZNSt8__detail15_List_node_base7_M_hookEPS0_
    Referenced from: /Users/vmittal3/usr/local/bin/long_spanning_reads
    Expected in: /usr/lib/libstdc++.6.dylib

    Is this the reason I didn't get anything in output bed files? If so any suggestions for the solution please?
    I am using TopHat version 1.3.3 on Mac OSx 10.6.
    Thanks.
    Tags: tophat error empty
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