I have been using the Diamond/MEGAN workflow for calculating the LCA.
And when I open MEGAN, I can see the taxonomic results, but if I use the program blast2lca with this command
./blast2lca -i 201.fna.daa -v -oro false
I cannot get any taxonomic information at all:
$ cat 201.fna-taxonomy.txt
ERR771073.575439-HWI-M02024:102:000000000-ABT8N:1:2102:10137:12295-1_1_445_+; ; Not assigned; 100;
ERR771073.1053164-HWI-M01108:56:000000000-ABT7L:1:2115:9056:12531-1_1_305_-; ; Not assigned; 100;
ERR771073.760095-HWI-M02024:102:000000000-ABT8N:1:2112:13907:7079-1_1_340_+; ; Not assigned; 100;
ERR771073.658829-HWI-M02024:102:000000000-ABT8N:1:2106:25997:21360-1_1_311_+; ; Not assigned; 100;
ERR771073.1049237-HWI-M01108:56:000000000-ABT7L:1:2114:23166:12399-1_1_348_+; ; Not assigned; 100;
ERR771073.798237-HWI-M02024:102:000000000-ABT8N:1:2114:20847:5930-1_1_300_+; ; Not assigned; 100;
ERR771073.359784-HWI-M02024:102:000000000-ABT8N:1:1110:12924:10580-1_1_268_-; ; Not assigned; 100;
ERR771073.286547-HWI-M02024:102:000000000-ABT8N:1:1106:2723:14156-1_1_451_+; ; Not assigned; 100;
ERR771073.1022416-HWI-M01108:56:000000000-ABT7L:1:2107:10939:11615-1_1_488_-; ; Not assigned; 100;
ERR771073.757315-HWI-M02024:102:000000000-ABT8N:1:2112:12360:3488-1_59_358_-; ; Not assigned; 100;
ERR771073.209126-HWI-M02024:102:000000000-ABT8N:1:1102:6910:12576-1_1_236_-; ; Not assigned; 100;
ERR771073.790465-HWI-M02024:102:000000000-ABT8N:1:2113:8386:18745-1_1_388_+; ; Not assigned; 100;
ERR771073.695286-HWI-M02024:102:000000000-ABT8N:1:2108:9719:19572-1_1_312_+; ; Not assigned; 100;
ERR771073.110460-HWI-M02024:104:000000000-ABR2C:1:2117:22897:19554-1_1_379_-; ; Not assigned; 100;
ERR771073.508040-HWI-M02024:102:000000000-ABT8N:1:1117:11838:24476-1_1_373_+; ; Not assigned; 100;
ERR771073.1063662-HWI-M01108:56:000000000-ABT7L:1:2118:12153:6988-1_1_214_-; ; Not assigned; 100;
ERR771073.465829-HWI-M02024:102:000000000-ABT8N:1:1115:24078:20491-1_1_160_+; ; Not assigned; 100;
ERR771073.309925-HWI-M02024:102:000000000-ABT8N:1:1107:9651:19187-2_1_256_-; ; Not assigned; 100;
Can you help me out if I made a mistake somewhere?
Here is the output of blast2lca
./blast2lca -i 201.fna.daa -v -oro false
Blast2LCA - Applies the LCA alignment to reads and produce a taxonomic classification
Options:
Input
--input: .../201.fna.daa
--format: Unknown
--mode: Unknown
Output
--output: .../201.fna-taxonomy.txt
--keggOutput: .../201.fna-kegg.txt
Functional classification:
--kegg: false
Output options:
--showRanks: true
--officialRanksOnly: false
--showTaxIds: false
Parameters
--minScore: 50.0
--maxExpected: 0.01
--topPercent: 10.0
--minPercentIdentity: 0.0
--maxKeggPerRead: 4
--applyTopPercentKegg: true
Classification support:
--parseTaxonNames: true
Other:
--firstWordIsAccession: true
--accessionTags: gb| ref|
--verbose: true
Version MEGAN Community Edition (version 6.12.5, built 25 Sep 2018)
Copyright (C) 2018 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Loading ncbi.map: 1,787,384
Loading ncbi.tre: 1,787,388
Loading kegg.map: 100,399
Loading kegg.tre: 106,785
Reading file: .../201.fna.daa
Writing file: .../201.fna-taxonomy.txt
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (3.3s)
Reads in: 18
Reads out: 18
Time: 14s