There have been several bug reports stating that meganization hangs on some DAA files. We have analyzed this issue and it appears to happen when very large numbers of alignments appear on the same segment of a query. To address this, a new update of MEGAN6 and the latest alpha version of MEGAN7 now contain an additional filter that uses only the first 250 alignments for any start/end pair in the query sequence. In other words, for a given query, during meganization, the program will use at most 250 alignments that start and stop at the same positions in a given query, all others will be ignored.
(In the UE versions, you can change this default to 1000, say, by typing the command
setprop max-number-of-alignments-on-same-query-interval=1000
using the “enter command” dialog.)