Continuing the discussion from Extracting reads from selected node:
I am using the Compare mode of MEGAN6 CE v6.8.18 to analyse my samples. I tried extracting a node into a different file in this mode, but it gave me an error - Execute failed: unknown Blast mode: Classifier. How do I get this working?
I use diamond to align my protein files to the NR database and then command-line tools to meganize my files. I’ve never used the Blastmode flag, and by default the value for this flag should be ‘Unknown’. However, its value has been set to ‘Classifier’ for all my runs. I need that normalized data for particular nodes. Is there any solution to this problem?
I failed to reproduce the issue, can you please give me more details, perhaps send me the comparison file
I have attached a comparison file here for you to assess.
Comparison.megan (133.9 KB)
Also, I use diamond for alignment (converting .daa files to .tab) and then blast2rma to meganize the .tab file as follows:
blast2rma -r read file (.faa) -i .tab file -o output file (.rma) -a2t taxonomy mapping file -a2eggnog eggNOG mapping file -a2interpro2go INTERPRO2GO mapping file -f BlastTab -ram readMagnitude -fun EGGNOG INTERPRO2GO -v
Among the flags for blast2rma, there is one called BLASTmode. Ideally, the default value for this flag should be ‘Unknown’, but that’s not happening. The value for this is being set to ‘Classifier’ by default, and I’m getting this error when I try to extract a node to a different file in the comparison mode.
To avoid this problem, I have started defining the value for BLASTmode parameter in blast2rma and that works, but I have a lot of data that I have processed that has the ‘Classifier’ issue. Is there any solution to this problem?
The blast mode here is BlastX (because you aligned DNA reads to a protein reference database).
However, rather than converting DAA format to BlastTab format, I suggest that you “meganize” the DAA file.
This process adds an additional block to the end of the DAA file that contains all the classification information for the file.
If you later want only a small summary file of the data (and not the whole DAA) file then you can use File->Export->Summary File to create one.