I am using the MEGAN Community Edition (version 6.12.6, built 15 Oct 2018) and use it to meganize DAA files created with diamond version 0.9.10. When I meganized the daa files everything workes perfect, but I can’t extract reads, MEGAN say that it have extracted the reads but no files are created. My supervisor have the same problem with that version of MEGAN.
I address the same issue with my data. I’m trying to extract reads (including summarized) from a node the following procedure:
MeganizeDAA file > (select node of interest) > right click > Extract Reads > check box “Include Summarized Reads” > Select output folder (Desktop) > name output file > Extract
The information displayed in message window are:
Executing: close what=current;
Info: Number of reads written: 5905197
Info: Command completed (170s): extract what=reads outdir='C:\Users\user\Desktop\reads'
outfile='eukar_R1.fasta' data=Taxonomy ids= 2759 allBelow=...
I have the same issues with my MEGAN CE (version 6.13.5, built 7 Jan 2019). I was unable to extract reads using the “extract reads for the selected nodes” tab on the tool bars. However, I could extract reads from File > export > reads.