[roliwilhelm]

Hi jtamames,

I hate to say it, but that is probably the topic of a new thread. If you have exhausted your trouble-shooting, I'd open a new thread and detail the error and what you've attempted. Then, contact Dr. Daniel Huson and include a link to your thread so that Dr. Huson's response may be of benefit to the community.

Thanks!

[Daniel.Huson]

How to save functional counts using command line MEGAN

[QUOTE=jtamames;150694]
To save functional counts using MEGAN in command line requires that the corresponding functional viewer is opened, using the command
show window=KeggViewer; (or CogViewer or SeedViewer).

The following script opens a file, shows the KeggViewer, sets the command "context" to the KeggViewer, uncollapses the tree, selects all the leaves and then exports counts for KEGG paths.

open file='/Users/huson/tmp/data.rma';
show window=KeggViewer;
set context=KeggViewer;
update;
uncollapse nodes=all;
select nodes=leaves;
export what=CSV format=keggpath_count separator=tab file='/Users/huson/tmp/counts.txt';
quit;

[felipelira3]

Can not export KEGG annotations

Hi Daniel,

I tried to use example to export but it doesn't work. My command file contains this:

open file='all_samples.CARD.daa.m8.reduced.contigs_names.fasta.daa.m8.with_filename.rma';
show window=KeggViewer;
set context=KeggViewer;
update;
uncollapse nodes=all;
select nodes=leaves;
export what=CSV format=keggpath_count separator=tab file='all_samples.CARD.daa.m8.reduced.contigs_names.fasta.daa.m8.with_filename.rma.out_kegg';
quit;

The output was this:

Command: set context=KeggViewer;
Executing: set context=KeggViewer;
Context set to: KeggViewer
Command: update;
Executing: update;
updating Kegg viewer
kegg2data: 0
Induce KEGG tree, keeping 0 of 30787 nodes for 0 classes
No KEGG data available
Command: uncollapse nodes=all;
Executing: uncollapse nodes=all;
kegg2data: 0
Induce KEGG tree, keeping 0 of 30787 nodes for 0 classes
No KEGG data available
Command: select nodes=all;
Executing: select nodes=all;
Number of nodes selected: 1
Command: export what=CSV format=keggpath_count separator=tab file='out_kegg';
Executing: export what=CSV format=keggpath_count separator=tab file='out_kegg';
Export in CSV format: Initializing
KEGG to counts
done 1
Message - Wrote 1 line(s) to file: out_kegg
Command: quit;
Executing: quit;

And the content of my output file was a single line like this: "KEGG;"

[Daniel.Huson]

It looks like you are using MEGAN5, please consider using MEGAN6.
Unfortunately, don't have time to fix MEGAN5 issues, but are you sure that your file has KEGG assignments? That might be the problem.

[felipelira3]

MEGAN5 instead of MEGAN6

Hi Daniel,
I am using MEGAN5 with the most actual mapping file. Using it at the interactive mode I can determine the KEGG annotation. The problem is when I use it by command line. I will try to use MEGAN6 by command line.