EggNog and Interpro2go mapping not working

Hello there. I am using MEGAN6 Linux on .sam files obtained with MagicBlast on a database of bacterial genomes (and plasmids) obtained converting NCBI files to FastA. The identifier is hence Accession Number of the NCBI Bacterial Genomes (NC_* and NZ_*) and the Taxonomy assignment works fine.

The problem is with mapping to Eggnog and Interpro2go after having loaded the appropriate files acc2eggnog-June2016X.abin and acc2interpro-June2016X.abin from MEGAN6.

As highlighted in the MEGAN log below, I don’t obtain any result for these two functional mappings, but this is really surprising !! How can it be ? Any suggestion ?

Also, I would like to know if the taxonomy mapping rate of these sequences (around 500.000 against a database of 10.135 target sequences) is reasonable.

Thanks in advance & best regards,

Alessandro Guffanti

Opening startup files
Loading 1,482,060
Loading ncbi.tre: 1,482,063
Induced tree has 1,482,063 of 1,482,063 nodes
Executing: show window=ImportBlast;
Loading 30,875
Loading eggnog.tre: 30,985
Loading 12,011
Loading interpro2go.tre: 27,675
Executing: load mapFile=’/bigstorage/analyses/Metagenomica/Seqs/acc2eggnog-June2016X.abin’ mapType=Accession cName=Taxonomy;
Opening file: /bigstorage/analyses/Metagenomica/Seqs/acc2eggnog-June2016X.abin
Executing: use mapType=Accession cName=Taxonomy state=false;
Executing: use cViewer=Taxonomy state=true;
Executing: use mapType=Accession cName=Taxonomy state=true;
Executing: load mapFile=’/bigstorage/analyses/Metagenomica/Seqs/nucl-acc2taxid-August2016.abin’ mapType=Accession cName=Taxonomy;
Opening file: /bigstorage/analyses/Metagenomica/Seqs/nucl-acc2taxid-August2016.abin
Executing: load mapFile=’/bigstorage/analyses/Metagenomica/Seqs/acc2eggnog-June2016X.abin’ mapType=Accession cName=EGGNOG;
Opening file: /bigstorage/analyses/Metagenomica/Seqs/acc2eggnog-June2016X.abin
Executing: load mapFile=’/bigstorage/analyses/Metagenomica/Seqs/acc2interpro-June2016X.abin’ mapType=Accession cName=INTERPRO2GO;
Opening file: /bigstorage/analyses/Metagenomica/Seqs/acc2interpro-June2016X.abin
Executing: import blastFile=’/bigstorage/analyses/Metagenomica/Seqs/SRR029686.TS19.nt.sam’ fastaFile=’/bigstorage/analyses/Metagenomica/Seqs/SRR029686.TS19.fasta’ meganFile=’/bigstorage/analyses/Metagenomica/Seqs/SRR029686.TS19.nt.rma6’ useCompression=true format=SAM mode=BlastN maxMatches=100 minScore=50.0 maxExpected=0.01 minPercentIdentity=0.0 topPercent=10.0 minSupportPercent=0.01 minSupport=1 weightedLCA=false weightedLCAPercent=80.0 minComplexity=0.0 useIdentityFilter=false fNames=EGGNOG INTERPRO2GO paired=false;
Classifications: Taxonomy,EGGNOG,INTERPRO2GO
Parsing file: /bigstorage/analyses/Metagenomica/Seqs/SRR029686.TS19.nt.sam
Total reads: 469,005
Alignments: 728,194
Total reads: 469,005
With hits: 190,753
Alignments: 728,194
Assig. Taxonomy: 189,195
Assig. EGGNOG: 0
MinSupport set to: 19
Min-supp. changes: 203
Numb. Tax. classes: 124
Numb. EGG. classes: 1
Numb. INT. classes: 1
Class. Taxonomy: 124
Class. EGGNOG: 1
Induced tree has 196 of 1,482,063 nodes
Induced tree has 196 of 1,482,063 nodes
Info: Command completed (104s): import blastFile=’/bigstorage/analyses/Metagenomica/Seqs/SRR029686.TS19.nt.sam’ fastaFile=’/bigstorage/analyses/Metagenomica…
Executing: open viewer=INTERPRO2GO;
Induced tree has 2 of 27,675 nodes
Induced tree has 2 of 27,675 nodes

The taxonomic assignment rate looks ok
You are not getting any assignments to EGGNOG or INTERPRO because they require that you again against protein reference sequences, not DNA.