Dear Dr.Daniel and everyone,
I use DIAMOND and MEGAN for the first time to analyze my sample from soil in HPCC server. I’ve got DAA file and I want to convert it into the RMA file.
I’ve download database from MEGAN download page
and then I convert the file following the generic pipeline for DIAMOND and MEGAN6, but it doesn’t work.
I also read this thread http://megan.informatik.uni-tuebingen.de/t/kegg-data-for-daa2rma-command/1366?u=lulunisrna
from that thread I get that I didn’t need to use parameters parameters such as
--acc2taxa, --acc2eggnog and --acc2interpro2go but I can use --mapDB parameter.
But, when I run the command line with --map parameter it’s doesn’t work.
And then, I tried to run with this command line
daa2rma -i alignment/HA_result.daa -o megan/HA_result.rma and it’s work.
I got the result like this:
Version MEGAN Community Edition (version 6.12.3, built 14 Aug 2018) Copyright (C) 2018 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY. Loading ncbi.map: 1,787,384 Loading ncbi.tre: 1,787,388 In DAA file: alignment/HA_result.daa Output file: megan/HA_result.rma Classifications: Taxonomy Parsing file: alignment/HA_result.daa 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (1312.4s) Total reads: 1,032,425 Alignments: 6,618,743 100% (0.0s) Binning reads: Initializing... Initializing binning... Using 'Naive LCA' algorithm for binning: Taxonomy Binning reads... Binning reads: Analyzing alignments Total reads: 1,032,425 With hits: 1,032,425 Alignments: 6,618,743 Assig. Taxonomy: 0 MinSupport set to: 516 Binning reads: Applying min-support & disabled filter to Taxonomy... Min-supp. changes: 0 Binning reads: Writing classification tables Numb. Tax. classes: 1 Binning reads: Syncing Class. Taxonomy: 1 100% (1034.5s) Total time: 2357s Peak memory: 2.0 of 2.1G
I don’t know the result is true or false for the analysis because I also read threads from MEGAN and the output is not like my output that I get.
Pleas guide me and give me an advice.
Thank you for your help.