input parsing error

[kirti prakash]

Hi,

I am using latest version of Sate with default settings, and sate
reports 'input parsing error, on line X at column Y, unrecognised
sequence symbol "T"'. Also, sometimes it quits unexpectedly without
any error reports.

I can provide details and link to the fasta file, if required. I am
wondering if this might be due to some constraint on header of fasta
file ? A typical header in the fasta file looks like the following.
>Oncidium Gower Ramsey
AATTGGGCCC....

There are 155 sequences, each being around 100kb in length. The mac
version I am using is 10.7.3, and it has 2x 2.66 GHz 6-core intel Xeon
processors with 24 GB memory. Any help on this would be greatly
appreciated.

Thanks,
Kirti

[Mark Holder]

Hi Kirti,
Hmmm. There should not be a constraint on the names (though the first character in the line of each name should be '>' to '|').


If you send the input file to mtho...@ku.edu we will give you files a try on our machines and try to troubleshoot this issue.

Using my email address for the file will keep your dataset off this public list.


thanks,
mark holder

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