To use a gff file as reference in MIRA make sure the nucleotide sequence is embedded in the file, then it should work. (most gff files out there, including those from NCBI, don't contain any sequence)
Andrej On 10/23/2014 10:02 AM, Felipe Lira wrote:
THank you guys. You are awesome. To fix this I used the .gbk file to map my reads and it worked.I will try to put name and sources of each file to use .gff file with mira.To clarify, what I tried to do initially was to use a .gff file to map the reads but it did not work, so I tried to convert to ".gff3" thinking that it would be better but not. For this, I became to .gbk file to map all reads.In any case, thank you for all and I am sorry to mix the thread with different subjects.Felipe Lira Spanish National Center of Biotechnology - CNB/ CSIC /Microbial Biotechnology Department/ Fellow of http://obrasocial.lacaixa.es/Antes de imprimir este mensaje piense bien si es realmente necesario hacerlo./Before you print this e-mail, think well if it is //really// necessary./El Jueves 23 de octubre de 2014 8:53, Andrej Benjak <abenjak@xxxxxxxxx> escribió:>> miraconver -f gbk -t gff3 NC_xxxx.gbk NC_xxxx.gff3 I deduce the problem was in converting a GenBank file to a gff3. >> GFF file '../NC_017671.gff' had unrecoverable errors (see output above).I downloaded the NC_017671.gbk and tried to convert it to gff3. I also get an error:miraconvert -f gbk -t gff3 NC_017671.gbk test Loading from gbf, saving to: gff3 Loading data from gbf ... Internal logic/programming/debugging error (*sigh* this should not have happened) ******************************************************************************** * gff3 file stream not open??? * ********************************************************************************->Thrown: void ConvPro::saveReadPool(ReadPool & rp, list<ofstream *> & ofs)->Caught: int mainConvPro(int argc, char ** argv) Aborting process, probably due to an internal error. If you want to report the error, please do so on http://sourceforge.net/p/mira-assembler/tickets/ and also give a short notice on the mira talk mailing list.If reporting, please do not delete the log and checkpoint directories, there maybe files in them which could be needed to find the problem.Subscribing / unsubscribing to mira talk, see: //www.freelists.org/list/mira_talkCWD: /home/abenjak/Downloads Thank you for noticing that this is *NOT* a crash, but a controlled program stop. I tried the same with another GenBank file, and I got the same error. Andrej On 10/22/2014 10:22 PM, Bastien Chevreux wrote:On 22 Oct 2014, at 19:09 , Felipe Lira <felipelira3@xxxxxxxxxxxx <mailto:felipelira3@xxxxxxxxxxxx>> wrote:I think that the title of this email is not so clear.The whole thread has become bit unclear to me :-)The comand was:Looks like something is in the gff3 file which the GFF3 parser of MIRA does not like. It’s very well possible that it’s a bug. Maybe if you gave the names and sources of the files you used plus the commands you ran I might have a better idea of what went wrong.B.
