Can't extract reads

Hello Megan,

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.

Best regards/

I have just checked, File->Extract reads works for me for the named version of MEGAN CE.

Could you send me the messages that appear in the message window.

As a work-around, use File->Export->Export Reads…

Hello Daniel,

It just say “numer of reads written: e.g.299” but no file with the

reads is created. I click on the node of the tree with the species

I want, right click and choose extract reads. Everything looks

correct in the terminal but, again, no file with reads is created.

I forgot to mention that I use the

MEGAN_Community_macos_6_12_6.dmg<>, and then meganize the DAA files with the<>.

Best regards/


Please select, copy and paste the contents of the Message Window so I can see what MEGAN is reporting…


I am experiencing the same issue here. I am extracting reads and the command line tells me this has been done without error but the file is not created.
Has this issue been solved somehow?

Thank you fro any reply,

I am using Megan community edition 6.14.2.
And my input is a .daa file as well as the corresponding .fasta.
The accession file is prot_acc2tax-Nov2018X1.abin.

Info: Command completed (216s): import blastFile=’/blastp_chunks_new/input_file.chunk_000.daa’ …
Induced tree has 908 of 2,031,708 nodes
Induced tree has 908 of 2,031,708 nodes
Executing: show window=ExtractReads;
Executing: set summarized=true;
Executing: extract what=reads outdir=’/blastp_chunks_new’ outfile=‘000_Prok.fasta’ data=Taxonomy ids= 2 2157 allBelow=true;
Info: Number of reads written: 68228
Info: Command completed (15s): extract what=reads outdir=’/blastp_chunks_new’ outfile='000_Prok…
Executing: collapse nodes=selected;


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 use the MEGAN CE version 6.14.2.

Thank you in advance!


This specification of the output directory looks questionable. Do you really have a directory called blastp_chunks_new that is placed at the very top of the directory structure?

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.