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
