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#251 pacBioToCA fails at trimFastqByQVWindow

correction
closed-out-of-date
nobody
None
5
2014-04-04
2013-08-01
Josh
No

I am running pacBioToCA (from CVS) and getting the error message "Error, header files are not equal" from trimFastqByQVWindow.

This occurs when I restart pacBioToCA after removing runPartition.sh (as directed by the error message produced by the first run).

I ran 'grep ">"' on the corrected.fasta and corrected.qual files in the temp directory and confirmed (by diff) that the headers are identical.

Thanks for the help.

Josh

Discussion

  • Sergey Koren
    Sergey Koren
    2013-08-05

    There was a bug in trimFastqByQVWindow with fasta/qual files over 4GB. In those cases, the file was truncated, causing the different header files error message. The bug was fixed on 2013-05-28. Please update the code to this date or more recent to see if the error is fixed. You should be able to just re-run trimFastqByQVWindow.

     
  • Sergey Koren
    Sergey Koren
    2014-04-04

    • status: open --> closed-out-of-date