Fix for "disk I/O error" or running without SQLite

[Camilla Ip]

Hi,

I am trying to use Ruffus 2.6.3 on a system where SQLite might not be installed correctly and cannot be fixed.

I keep getting errors like:

Original exception:

    Exception #1
      'sqlite3.OperationalError(disk I/O error)' raised in ...
       Task = def Step1(...):


    Traceback (most recent call last):
      File "/PATH/TO/python2/4.2.0/lib/python2.7/site-packages/ruffus/task.py", line 2519, in _is_up_to_date
        verbose_abbreviated_path=verbose_abbreviated_path)
      File "/PATH/TO/python2/4.2.0/lib/python2.7/site-packages/ruffus/file_name_parameters.py", line 548, in needs_update_check_modify_time
        if os.path.relpath(p) not in job_history and p not in set_incomplete_files:
      File "/PATH/TO/python2/4.2.0/lib/python2.7/_abcoll.py", line 388, in __contains__
        self[key]
      File "/PATH/TO/python2/4.2.0/lib/python2.7/site-packages/ruffus/dbdict.py", line 174, in __getitem__
        (key, )).fetchone()
    OperationalError: disk I/O error

Is there an easy way to fix this error?
Or could this version of Ruffus be run without SQLite?

Many thanks in advance,
Camilla

-- 
Dr Camilla Ip
Bioinformatician, Barnes Group, Peter Medawar Building for Pathogen Research
Academic Visitor, Wellcome Trust Centre for Human Genetics
University of Oxford, UK
E: camil...@gmail.com camil...@well.ox.ac.uk