KEGG comparison to BIOM output


#1

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;