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  • #1

    CREST extractSClip.pl Error

    Hi All
    I am getting the following error when I am trying to run "extractSClip.pl" from CREST package on a specific bam file. It runs fine on others! Here is the command and error:

    command:
    ./extractSClip.pl -i /backup/cell-line/c727c60e-8ddd-1ddc-e040-ad451e414a77/G15511.HCC1143.2.bam -o /backup/cell-line/crest-out --ref_genome hg19.fa

    Error:
    substr outside of string at /usr/local/lib64/perl5/Bio/DB/Bam/AlignWrapper.pm line 280.
    Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/DB/Bam/AlignWrapper.pm line 280.



    Any help is appreciated.

    Thanks
    M_A
    Tags: alignwrapper.pm, crest, extractsclip.pl
  • #2
    Hi,

    did you manage to solve this issue in the end? I'm getting the same error message today!

    Thanks,

    Chiara

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