[Biopython-dev] [Bug 3102] Error converting sff into fastq

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3102


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
            Summary|Error converting sff into   |Error converting sff into
                   |fastaq                      |fastq




------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2010-06-18 09:45 EST -------
Thanks Chris.

Giorgio - Could you confirm which version of Biopython are you using?

To me the error message suggests the SFF file is corrupted (damaged). Is it
very large? Could you attach it to this bug (or email it to me personally) to
check?

Have you been able to process the SFF file with any other tools (e.g.
sff_extract which should work on Windows/Linux/Mac, or the Roche tools which
are Linux only)?

If you copied the SFF file over your network, or over the internet from your
sequencing center, perhaps there was an error there. Could you try
re-downloading the SFF file?

Regards,

Peter


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