In Megan 6.12.3UE, I am trying to extract the KEGG comparison of two samples in command line mode to BIOM file. How do I select all the nodes in the KEGG view? My failed output is below. Very grateful if you could pls advise suitable commands.
MEGAN> Command: compare mode=RELATIVE readAssignmentMode=readCount keep1=false ignoreUnassigned=true meganFile='/home/data/mmeg_sarisa/Transcriptomics/pipeline/March/extract/3700/RS-C-BS-1M.rma', '/home/data/mmeg_sarisa/Transcriptomics/pipeline/March/extract/3700/RS-V-BS-1M.rma';
Executing: compare mode=RELATIVE readAssignmentMode=readCount keep1=false ignoreUnassigned=true meganFile='/home/data/mmeg_sarisa/Transcriptomics/pipeline/March/extract/3700/RS-C-BS-1M.rma', '/home/data/mmeg_sarisa/Transcriptomics/pipeline/March/extract/3700/RS-V-BS-1M.rma';
Executing: open file='/home/data/mmeg_sarisa/Transcriptomics/pipeline/March/extract/3700/RS-C-BS-1M.rma' readOnly=true;update;
Loading MEGAN File: RS-C-BS-1M.rma
Info: Opened file '/home/data/mmeg_sarisa/Transcriptomics/pipeline/March/extract/3700/RS-C-BS-1M.rma' with 210,986 reads
Executing: update;
updating viewer
Induced tree has 50 of 1,787,388 nodes
Induced tree has 50 of 1,787,388 nodes
updating viewer
Induced tree has 50 of 1,787,388 nodes
Induced tree has 50 of 1,787,388 nodes
10% Executing: open file='/home/data/mmeg_sarisa/Transcriptomics/pipeline/March/extract/3700/RS-V-BS-1M.rma' readOnly=true;update;
Loading MEGAN File: RS-V-BS-1M.rma
Info: Opened file '/home/data/mmeg_sarisa/Transcriptomics/pipeline/March/extract/3700/RS-V-BS-1M.rma' with 432,400 reads
Executing: update;
updating viewer
Induced tree has 56 of 1,787,388 nodes
Induced tree has 56 of 1,787,388 nodes
updating viewer
Induced tree has 56 of 1,787,388 nodes
Induced tree has 56 of 1,787,388 nodes
20% Computing comparison:
Normalizing to: 210385 reads per sample
10% Total assigned: 420,771 normalized
100% (9.5s)
updating viewer...
MEGAN> Command: openUE viewer=KEGG;
Executing: openUE viewer=KEGG;
Loading kegg.map: 22,161
Loading kegg.tre: 56,595
MEGAN> Command: uncollapse nodes=all;
Executing: uncollapse nodes=all;
Induced tree has 55 of 1,787,388 nodes
Induced tree has 55 of 1,787,388 nodes
**MEGAN> Command: select id =-4; select nodes=subTree;**
**Executing: select id =-4; select nodes=subTree;**
**Number of nodes selected: 0**
MEGAN> Command: export format=biom data=KEGG file='/home/data/mmeg_sarisa/Transcriptomics/pipeline/March/compare/compare.biom';
Executing: export format=biom data=KEGG file='/home/data/mmeg_sarisa/Transcriptomics/pipeline/March/compare/compare.biom';
No nodes selected
Command usage: export format=biom data={EGGNOG|INTERPRO2GO|KEGG|PFAM|SEED|Taxonomy} file=<filename> [officialRanksOnly={true|false}]; - Export data in BIOM 1.0.0 (JSON) format (see http://biom-format.org/documentation/format_versions/biom-1.0.html)
Error: Command failed: No nodes selected
MEGAN> Command: close; quit;
Executing: close; quit;
Executing: quit;