When importing a blastn file into MEGAN6 UE, a cladogram is drawn to the main viewer that reflects the taxonomy of the sample as expected.
However, when running from the command line, as below, I get a cladogram showing only nodes for “no hits” and “not assigned” as if MEGAN did not read the ncbi nucleotide taxonomy files. It is my understanding that these are loaded automatically when MEGAN starts. What am I doing wrong? Also is there a collection of MEGAN command line script examples somewhere?
>MEGAN -g
MEGAN> import blastFile='/project/MA_contamination/work/data/julies/noMap.100.fasta-vs-nt.1e-5.blastn' fastaFile='/project/MA_contamination/work/data/julies/noMap.100.fasta' meganFile='/project/MA_contamination/work/data/julies/noMap.100.fasta-vs-nt.1e-5-2.commandline.rma6' useCompression=true format=BlastText mode=BlastN maxMatches=100 minScore=50.0 maxExpected=0.01 minPercentIdentity=0.0 topPercent=10.0 minSupportPercent=0.05 minSupport=1 lcaAlgorithm=naive minPercentReadToCover=0.0 minPercentReferenceToCover=0.0 minComplexity=0.0 useIdentityFilter=false readAssignmentMode=readCount fNames=Taxonomy ;
Command: import blastFile='/project/MA_contamination/work/data/julies/noMap.100.fasta-vs-nt.1e-5.blastn' fastaFile='/project/MA_contamination/work/data/julies/noMap.100.fasta' meganFile='/project/MA_contamination/work/data/julies/noMap.100.fasta-vs-nt.1e-5-2.commandline.rma6' useCompression=true format=BlastText mode=BlastN maxMatches=100 minScore=50.0 maxExpected=0.01 minPercentIdentity=0.0 topPercent=10.0 minSupportPercent=0.05 minSupport=1 lcaAlgorithm=naive minPercentReadToCover=0.0 minPercentReferenceToCover=0.0 minComplexity=0.0 useIdentityFilter=false readAssignmentMode=readCount fNames=Taxonomy ;
Executing: import blastFile='/project/MA_contamination/work/data/julies/noMap.100.fasta-vs-nt.1e-5.blastn' fastaFile='/project/MA_contamination/work/data/julies/noMap.100.fasta' meganFile='/project/MA_contamination/work/data/julies/noMap.100.fasta-vs-nt.1e-5-2.commandline.rma6' useCompression=true format=BlastText mode=BlastN maxMatches=100 minScore=50.0 maxExpected=0.01 minPercentIdentity=0.0 topPercent=10.0 minSupportPercent=0.05 minSupport=1 lcaAlgorithm=naive minPercentReadToCover=0.0 minPercentReferenceToCover=0.0 minComplexity=0.0 useIdentityFilter=false readAssignmentMode=readCount fNames=Taxonomy ;
Classifications: Taxonomy
Parsing file: /project/MA_contamination/work/data/julies/noMap.100.fasta-vs-nt.1e-5.blastn
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (0.5s)
Total reads: 100
Alignments: 2,147
100% (0.0s)
Initializing binning...
Using 'Naive LCA' algorithm for binning: Taxonomy
Binning reads...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (1.3s)
Total reads: 100
With hits: 71
Alignments: 2,147
Assig. Taxonomy: 0
MinSupport set to: 1
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (1.4s)
Min-supp. changes: 0
10% 20% Numb. Tax. classes: 2
100% (0.0s)
Class. Taxonomy: 2
MEGAN> update
Command: update
Executing: update;
100% (23.2s)
updating viewer...
Induced tree has 3 of 2,031,708 nodes
Induced tree has 3 of 2,031,708 nodes