Hi,
I am a newbie.
I have tried to use Diamond and Megan for several weeks but never managed to get a taxonomy assignment. Even though I saw many people posting about this issue, I can not manage to figure out what is the problem. Here is what I have done so far.
diamond makedb --in uniprot_sprot.fasta -d uniprot_sprot --taxonmap prot.accession2taxid --taxonnodes nodes.dmp
diamond blastx -d uniprot_sprot -q SRR6281583_1.fna -o SRR6281583_1.m8
diamond blastx -f 102 -d uniprot_sprot -q SRR6281583_1.fna -o SRR6281583_1-blastx.tax
According to Megan manual, concerning the -m8 BLAST output “However, if you add an additional column to this format containing the associated taxon name or numerical NCBI taxon-id for each line then MEGAN will parse these and use them as input.”
I joined the m8 and the tax files but that did not do the trick.
In Megan, I am using the files from the mega download page, prot_acc2tax-Nov2018X1.abin
acc2interpro-June2018X.abin
acc2eggnog-Oct2016X.abin
acc2seed-May2015XX.abin
In Megan window:
Executing: ‘import’‘blastFile’’=’’/Users/pierre/work/test1.txt’‘fastaFile’’=’’/Users/pierre/work/SRR6281583_1.fna’‘meganFile’’=’’/Users/pierre/work/test1.rma6’‘useCompression’’=’‘true’‘format’’=’‘BlastTab’‘mode’’=’‘Classifier’‘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’’=’‘EGGNOG’‘INTERPRO2GO’‘SEED’;
Classifications: Taxonomy,SEED,EGGNOG,INTERPRO2GO
Parsing file: /Users/pierre/work/test1.txt
Total reads: 307,050
Alignments: 7,400,961
Initializing binning…
Using ‘Naive LCA’ algorithm for binning: Taxonomy
Using Best-Hit algorithm for binning: SEED
Using Best-Hit algorithm for binning: EGGNOG
Using Best-Hit algorithm for binning: INTERPRO2GO
Binning reads…
Total reads: 307,050
With hits: 307,050
Alignments: 7,400,961
Assig. Taxonomy: 0
Assig. SEED: 0
Assig. EGGNOG: 0
Assig. INTERPRO2GO: 0
MinSupport set to: 153
Min-supp. changes: 0
Numb. Tax. classes: 1
Numb. SEED classes: 1
Numb. EGG. classes: 1
Numb. INT. classes: 1
Class. Taxonomy: 1
Class. SEED: 1
Class. EGGNOG: 1
Class. INTERPRO2GO: 1
Info: Command completed (581s): ‘import’‘blastFile’’=’’/Users/pierre/work/test1.txt’‘fastaFile’’=’’/Users/pierre/work/SRR6281583_1.fna’‘meganFile’’=’’/Users…
Induced tree has 2 of 2,031,708 nodes
Induced tree has 2 of 2,031,708 nodes
I am now confused because I saw a post mentioning that the BLAST output should have 12 columns. How can we show taxonomy ID in the BLAST output without adding an additional column?
I have also created a daa file and meganized it but still no taxonomy assignment.
Executing: meganize daaFile=’/Users/pierre/work/SRR6281583_1-blastx.daa’ minScore=50.0 maxExpected=0.01 minPercentIdentity=0.0 topPercent=10.0 minSupportPercent=0.05 minSupport=1 lcaAlgorithm=naive minComplexity=0.0 useIdentityFilter=false readAssignmentMode=readCount fNames=EGGNOG INTERPRO2GO SEED longReads=false paired=false;
Meganizing file: /Users/pierre/work/SRR6281583_1-blastx.daa
Initializing binning…
Using ‘Naive LCA’ algorithm for binning: Taxonomy
Using Best-Hit algorithm for binning: SEED
Using Best-Hit algorithm for binning: EGGNOG
Using Best-Hit algorithm for binning: INTERPRO2GO
Binning reads…
Total reads: 307,050
With hits: 307,050
Alignments: 7,400,961
Assig. Taxonomy: 0
Assig. SEED: 0
Assig. EGGNOG: 0
Assig. INTERPRO2GO: 0
Min-supp. changes: 0
Class. Taxonomy: 1
Class. SEED: 1
Class. EGGNOG: 1
Class. INTERPRO2GO: 1
Thanks for your assistance.