Hi, I cannot get MEGAN to read the magnitudes in my headers, although I am importing a file pair (xml and fasta) that in some previous version of MEGAN resulted in magnitudes being read correctly. Can anyone see what the problem might be?
Megan Community 6.10.8
NZ.c.longer100.3pcfiltered.uniq.all.ali.ngs.goodFORMAGNITUDETEST.xml (1.4 MB)
NZ.c.longer100.3pcfiltered.uniq.all.ali.ngs.goodFORMAGNITUDETEST.fasta (7.3 KB)
I just tried your data, it works fine. My guess is that you did not set the “Read Assignment Mode” to “ReadMagnitude”.
You will find this feature in the LCA Params tab of the Import from Blast dialog.
Hi Daniel, Thanks for the response. I was trying with readMagntitude selected form the LCA parameters dialogue. But it only reads a magntiude of 12 (the number of OTUs), when it should be 1,255.
INFO: Reads=12 Assigned=12 (readMagnitude) MinScore=50.0 MaxExpected=0.01 TopPercent=10.0 MinSupportPercent=0.05 LCA=naive blast=BlastN
EDIT: Just updated to latest MEGAN version (6.10.11), but the problem persists
Ah, it works using the weighted algorithm. readMagnitude does not work with naive algorithm, is that correct? If so, would it be possible to add this feature? It helps when viewing the tree to visualize number of reads rather than number of sequences assigned to a node.
No, it works using any algorithm: You choose the “LCA algorithm”, e.g. “naive” separately from the “Read assignment mode”, e.g. “readMagnitude”, as can be seen here:
Thanks again, not sure what I was doing differently, but it is working for me now!
Just a note that I still have a small issue with this, but found that I generally have to click apply on the change LCA parameters dialogue two-three times before magnitude is read in properly. Not sure of the reason.