MEGAN5 - input blast -m8 option problem

Question

[fhsantanna]

Hi,

I am trying to run MEGAN5 using a blast table generated by an associated researcher.

I know that MEGAN is able to interpret blast files fomatted by the m8 option. I have tried to load the tables without success, and I believe that it is related to the field order of my tables.

Does anybody know the correct format of tabular tables that I must provide to MEGAN?

Thanks in advance.

Here is a sample of my tables:

# Fields:
query_id(sample     contig          start     end     strand     length)     subject_id       subject_function          subject_organism                    %_identity     %_positive     alignment_length     gaps     query_start     query_end     subject_start     subject_end     evalue          bit_score     taxonomy
6                   contig00001     1         411     0          136         WP_003253097     DNA_methyltransferase     Geobacillus_thermoglucosidasius     133            136            136                  0        1               136           2                 137             4.79761e-90     716           Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Geobacillus
6                   contig00001     439       3295    0          949         WP_003354162     DNA_methyltransferase     Bacillus_smithii                    585            613            642                  0        67              708           1                 642             0               3118          Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Bacillus
6                   contig00001     3472      3546    0          23          unknown          unknown                   unidentified

[fhsantanna]

I'll try to convert the original tables into the proper format.

[fhsantanna]

I have loaded the blast results following your tips. I have used an example file with three blast results. However, the resulting "tree" has had a root linked to a node with a "Not assigned" message, although I have loaded the gi_taxid_prot.bin file (from here) in the Taxonomy tab using the "load GI mapping file" button.

Here is my blast file:

01contig00001_1_491_+    gi|495059223|ref|WP_007784057.1|    29.94    157    100    4    9    157    4    158    2e-11    67.4
01contig00001_567_4372_+    gi|495059216|ref|WP_007784050.1|    56.09    624    262    7    348    967    5    620    0.0     711
01contig00001_4406_4776_+    gi|525334940|gb|AGR46604.1|    54.17    48    22    0    1    48    2    49    3e-12    66.6

Was MEGAN not supposed to utilize the gi_taxid_prot.bin file to assign a taxonomic label to each blast result?

Thanks again.

[Istvan Albert]

keep reading the manual, I don't recall the exact details but the tool can be finicky regarding the precise structure of the fields.

Load some example files and make sure to check the boxes that need checked when importing.

[fhsantanna]

I already did it. In fact, the manual informs that there are example files available in its website, but I was not able to find it. Could you please provide one of your blast files? So I could test in my machine.

Thanks.

Answer 1

[Istvan Albert]

I am not sure what it is called in the legacy blast but you need to use the default he tabular format. In blast+ it is -outfmt 6 or 7 format. And you should keep the default column orders. Yours seem to be different.

see the relevant entries for

blastn -help

[JC]

I agree, the blast output seem to be personalized/modified.