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  • BCL converter error

    Hi all,

    I'm trying to get the fast file from our demo PhiX run and I have some error in the nohup.out after make -j command

    here is the output - http://pastebin.com/x0VT9vEx

    so I got empty fastq.gz files
    ------------
    SMART - bioinfo.uni-plovdiv.bg

  • #2
    Here are the clues from your error log. At least two BCL files are missing from your data set.

    Code:
    File /mnt/storage/DATA/GAIIX/Data/Intensities/BaseCalls/L006/C1.1/s_6_1.bcl does not exist
    
    File /mnt/storage/DATA/GAIIX/Data/Intensities/BaseCalls/L008/C31.1/s_8_1.bcl does not exist
    To get around this problem you can use the "--ignore-missing-bcl" command line option for configureBclToFastq. This will interpret missing *.bcl files as no call.

    Comment


    • #3
      Thanks!

      I also noticed:


      Error: 2012-Nov-16 14:48:07: No such file or directory: /home/milev/CASAVA_v1.8.2/src/c++/lib/alignment/BclReader.cpp(86): Throw in function unsigned int casava::alignment::BclReader::readClusterCount()
      ------------
      SMART - bioinfo.uni-plovdiv.bg

      Comment

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