I’m trying to maganize one of my diamond daa file yet it was always killed during writing phase. I tried to enlarge the memory invoked however it didn’t work. Here is the verbose:
Version MEGAN Ultimate Edition (version 6.24.20, built 5 Feb 2023) Author(s) Daniel H. Huson Copyright (C) 2023 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY. Java version: 18.0.2.1 Functional classifications to use: EC, EGGNOG, GTDB, INTERPRO2GO, KEGG, SEED Loading ncbi.map: 2,396,736 Loading ncbi.tre: 2,396,740 Loading ec.map: 8,200 Loading ec.tre: 8,204 Loading eggnog.map: 30,875 Loading eggnog.tre: 30,986 Loading gtdb.map: 240,103 Loading gtdb.tre: 240,107 Loading interpro2go.map: 14,242 Loading interpro2go.tre: 28,907 Loading kegg.map: 25,480 Loading kegg.tre: 68,226 Loading seed.map: 961 Loading seed.tre: 962 Meganizing: ~/Documents/daa_origin/sample10.daa Meganizing init Annotating DAA file using FAST mode (accession database and first accession per line) Annotating references 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (149.8s) Writing 10% 20% 30% 40% 50% 60% 70% 80% 90% ~/megan/tools/daa-meganizer: line 38: 581947 Killed $java $java_flags --module-path=$modulepath --add-modules=megan6u megan6u.tools.DAAMeganizer $options
This looks like a memory issue. What is the size of the DAA file? How much memory did you assign to MEGAN? How much physical memory does the machine have? If you have a very large DAA file, say 50G, then you might need give 32G to MEGAN, say, but then also additional memory must be available for parts of the program that run “outside” of that assigned amount, at least another 32G, but more is better.
Thanks for your reply. The size of my daa file is 27GB and I assigned 500GB to MEGAN, capable for my physical memory. The strange thing is, even DAA files as large as 94GB could be successfully meganized on my workstation, this 27GB DAA file just cannot be meganized, always killed during writing phase.
which I was never able to solve (even when testing with 1 TB RAM). My idea was that I could use diamond+megan to classify contigs from a large metagenome assembly. Which would really help with this as other annotation tools are very slow. However, in the end this was not possible because daa-meganizer always gets stuck or fails at the writing step. So I had to go back to tools like PROKKA for metagenome assembly annotation.