Hi Darek, Always reply to the list, as I can't help you with this error; I'm a GFF person, not an Apollo developer. Perhaps Ed or someone else can help you with this.
Scott On Fri, Mar 5, 2010 at 3:37 PM, dar ked <[email protected]> wrote: > Dear Scott, > > thank you for such prompt answer. > I am sorry seems that I posted the previous version of the file. > This time I believe it should have just tabs. > > I am getting a different error (see attachment) but still Apollo will not > load it. > > Best wishes, > > Darek Kedra > > > --- On Fri, 3/5/10, Scott Cain <[email protected]> wrote: > >> From: Scott Cain <[email protected]> >> Subject: Re: [apollo] loadin gff3 CDS into apollo problem >> To: "dar ked" <[email protected]> >> Cc: [email protected] >> Date: Friday, March 5, 2010, 10:50 AM >> Hi Darek, >> >> It looks like you have spaces rather than tabs between most >> of your >> columns. GFF3 must have 9 tab delimited columns, but >> I think you only >> have tabs between columns 8 and 9, whereas the rest of the >> columns are >> separated by spaces. >> >> Scott >> >> >> On Fri, Mar 5, 2010 at 1:32 PM, dar ked <[email protected]> >> wrote: >> > Hello, >> > >> > I am having a problem with loading gff3-like(?) file >> into Apollo >> > 1.11.3. Changing "CDS" to "match" solves the >> problem, but making the output of this gene prediction >> program compatible with Apollo would be much more sensible. >> > >> > Below is uuencoded small gff3 file. >> > >> > If anybody can point to incompatible things / provide >> me with >> > version acceptable by Apollo that will be very >> helpful. >> > >> > Sincerely yours, >> > >> > Darek Kedra >> > PS the error is: >> > Exception in thread "Thread-55" >> apollo.dataadapter.NonFatalDataAdapterException: Invalid >> number of columns >> > at >> apollo.dataadapter.gff3.GFF3Entry.parseData(GFF3Entry.java:523) >> > at >> apollo.dataadapter.gff3.GFF3Entry.<init>(GFF3Entry.java:72) >> > >> > >> > >> > >> > >> > >> > _______________________________________________ >> > apollo mailing list >> > [email protected] >> > http://mail.fruitfly.org/mailman/listinfo/apollo >> > >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. >> >> scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) >> 216-392-3087 >> Ontario Institute for Cancer Research >> > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research _______________________________________________ apollo mailing list [email protected] http://mail.fruitfly.org/mailman/listinfo/apollo
