Problem with runs of Ns

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katharina
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Problem with runs of Ns

Post by katharina »

Originally posted in the old forum by Craig Wilding on 14.11.2013 - 17:46
Hi,
I am using Augustus for gene prediction from Anopheles mosquito scaffold data. Some of these scaffolds contain long runs of Ns and this seems to be causing a problem for Augustus - at least this is all I can see that is a problem. The file is approximately 105,000 lines long with 80 characters per line. Throughout the sequence there are strings of N of various lengths (10s, 100s) and most of these cause no problem. But at approximately line 103,000 I can get the file to work if I cut the file before a particular string of Ns but if it goes beyond this I get an error message: ||no input. Try again.
Is this a recognised problem and does anyone know how to solve it?
Thanks,
Craig
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katharina
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Re: Problem with runs of Ns

Post by katharina »

by Mario on 19.11.2013 - 10:27
I don't think it is the N's.
I suspect it is either a character encoding problem (What operating systems was this file saved under?) or a bug in the web server.
Augustus itself does not print "no input". I suspect, you are using the web server, right? In that case, can you please email me or Katharina Hoff the ID of the webserver job that produces the error message?
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