Hi Henrik You have found the correct solution. It is just that the blast reports coordinates from the start of the sequence and so they need joining up before you do the blast. I am not sure why you get that memory error. If you have access to another machine you may want to try the blast there. Alternatively you could possibly try a smaller number of contigs and then use the EMBOSS application 'union' to join them back up.
Regards Tim On 4/29/10 8:09 AM, "Henrik Lantz" <henrik.la...@mikrob.slu.se> wrote: > I was hoping I could get some help with a newbie Artemis question. Very new to > all this. > > I have made a denovo assembly of a fungus using MIRA and 454-data only. The > resulting fasta file with around 4000 contigs loads into Artemis fine. I can > check all the contigs, find ORFs etc. The problem appears when I want to > import the results of a blastall search on the contig-datafile. All > annotations from the blastall results are lumped into the first five contigs, > with the overwhelming majority in the first contig. Obviously not correct. I > am using the -m 8 flag for the blastall search. Looking through the resultfile > from blastall in a text editor I can see that the blastall search has worked, > and there are many interesting hits, but I would like to visualize the results > on the contigs. > > I read through the mail archive and found a user with a similar problem > (http://www.mail-archive.com/artemis-users%40sanger.ac.uk/msg00463.html) and > it seems one solution might be to save the contigs as a long continuous file > in Artemis, and then use that in the Blastall search. But when I try that I > get an error message from blastall: > > blastall(33748) malloc: *** mmap(size=1048576) failed (error code=12) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > Bus error > > I am running on MacOSX Snow Leopard with 20 GBs of memory. > Any help to get an inexperienced user started would be very much appreciated! > /Henrik > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
