Functional binning using blast2lca's acc2kegg mapping


#1

Hi Daniel and MEGAN team,

I’m trying to use blast2lca to get the KEGG KO output. I’m using my own mapping file (based off/generated from the KEGG linker files).

Below’s

  1. my command,
  2. tabbed blast (from diamond) and
  3. the mapping file (self generated)

I’ve relaxed the topPercent parameter --topPercent to 100.

As you can see the Diamond alignment subject’s IDs are in the mapping file. However I do not get any assignment. What is the problem here, did i miss something?

I’m using MEGAN CE 6.6.0 (2016) blast2lca.


Blast2lca Input cmd

./blast2lca -i input.m8 -f BlastTab -o output.tax -ko output.ko -k -a2kegg acc2ko -v  -top 100

the contents of input.m8

K00001|contig00001      ref|WP_011964898.1      75.9    390     94      0       1202    33      1       390     2.0e-179        636.3
K00001|contig00002      ref|WP_015908576.1      93.1    391     27      0       44      1216    1       391     1.2e-208        733.4
K00001|contig00002      ref|WP_011916279.1      91.8    391     32      0       44      1216    1       391     1.0e-207        730.3
K00001|contig00002      ref|WP_012547938.1      82.6    390     68      0       47      1216    3       392     1.3e-186        660.2
K00001|contig00002      ref|WP_012582733.1      80.3    390     77      0       47      1216    3       392     5.5e-182        644.8
K00001|contig00002      ref|WP_013624801.1      73.1    387     104     0       59      1219    3       389     5.9e-160        571.6
K00001|contig00002      ref|WP_013254033.1      64.3    384     137     0       59      1210    4       387     3.2e-137        496.1
K00001|contig00002      ref|WP_013297016.1      59.9    387     155     0       59      1219    5       391     4.6e-136        492.3
K00001|contig00003      ref|WP_011460576.1      100.0   400     0       0       1201    2       2       401     2.2e-231        808.9
K00001|contig00003      ref|WP_013297375.1      78.4    388     84      0       1165    2       3       390     6.2e-178        631.3
K00001|contig00003      ref|WP_014081290.1      66.5    388     130     0       1165    2       3       390     2.3e-148        533.1
K00001|contig00003      ref|WP_011170746.1      64.4    388     137     1       1165    2       3       389     2.4e-145        523.1
K00001|contig00003      ref|WP_013999256.1      64.2    388     138     1       1165    2       3       389     4.1e-145        522.3
K00001|contig00004      ref|WP_004682047.1      96.1    385     15      0       44      1198    1       385     1.3e-212        746.5
K00001|contig00004      ref|WP_006016282.1      95.8    385     16      0       44      1198    1       385     2.9e-212        745.3
K00001|contig00004      ref|WP_002965909.1      95.6    385     17      0       44      1198    1       385     1.9e-211        742.7
K00001|contig00004      ref|WP_004690269.1      95.6    385     17      0       44      1198    1       385     1.9e-211        742.7
K00001|contig00004      ref|WP_012093239.1      84.7    385     59      0       44      1198    1       385     6.0e-189        667.9

the mapping file

WP_011964898.1  1
WP_015908576.1  1
WP_011916279.1  1
WP_012547938.1  1
WP_012582733.1  1
WP_013624801.1  1
WP_013254033.1  1
WP_013297016.1  1
WP_011460576.1  1
WP_013297375.1  1
WP_014081290.1  1
WP_011170746.1  1
WP_013999256.1  1
WP_004682047.1  1
WP_006016282.1  1
WP_002965909.1  1
WP_004690269.1  1
WP_012093239.1  1

#2

Please remove the .1 suffixes from the mapping file, the parser can’t deal with them (it considers a dot to be a word boundary_
Or, alternatively, provide the file as a “synonyms” mapping file (but mapping using this mechanism is less efficient).
D


#3

got it,

thank you Daniel.