Export to CSV not working in MEGAN5


#1

Hi

I have a blastP report in XML format that I am trying to get taxonomy information for my reads from. I imported the XML file, collapsed at rank=‘Species’ and selected all nodes (no. of nodes = 1080172). I am trying to export this data to CSV by going to File -> Export -> CSV Format. But CSV format option is grayed out. I also tried to command line version but it says “Wrote 0 line(s) to file”. I have tried it on two different computers (Ubuntu and on a cluster). Following is the output of the last few lines of code.

Command: select nodes=all;
Executing: select nodes=all;
Number of nodes selected: 1080172
MEGAN> Command: export what=CSV format=readname_taxonpath separator=tab file='11_orfs_hmms/assembly.orfs.hmm.tax.txt';
Executing: export what=CSV format=readname_taxonpath separator=tab file='11_orfs_hmms/assembly.orfs.hmm.tax.txt';
Export in CSV format: Initializing
Read names to taxa
done 0
Message - Wrote 0 line(s) to file: assembly.orfs.hmm.tax.txt

What could be the issue here?


#2

please try using MEGAN6