ecotag: sequences not assigned
Hi,
I have successfully build up the trnL db and tried to use ecotag for assigning my sequnece to taxon, but I got mostly nothing:
[mingfei2@compute-7-3 ~]$ obi ecotag -m 0.97 --taxonomy ~/Mingfei/Fluidigm/US_Transect_Plant/us_transect/taxonomy/my_tax -R ~/Mingfei/Fluidigm/US_Transect_Plant/us_transect/trnL_db_97_1 ~/Mingfei/Fluidigm/US_Transect_Plant/us_transect/Std_final ~/Mingfei/Fluidigm/US_Transect_Plant/us_transect/Std_final_assigned_1
2021-02-24 15:57:38,264 [ecotag : INFO ] obi ecotag
Reading 2312342 taxa...
No local taxa
Building kmer tables... : Done
Building kmer tables... : Done
Done : 100 %
2021-02-24 15:57:52,112 [ecotag : INFO ] Done.
[mingfei2@compute-7-3 ~]$ obi less ~/Mingfei/Fluidigm/US_Transect_Plant/us_transect/Std_final_assigned_1
[mingfei2@compute-7-3 ~]$ obi stats ~/Mingfei/Fluidigm/US_Transect_Plant/us_transect/Std_final_assigned_1
2021-02-24 15:58:46,732 [stats : INFO ] obi stats
99.5 % |#################################################/ ] remain : 00:00:00
count total
184 472601
2021-02-24 15:58:46,791 [stats : INFO ] Done.
[mingfei2@compute-7-3 ~]$ obi stats -c SCIENTIFIC_NAME ~/Mingfei/Fluidigm/US_Transect_Plant/us_transect/Std_final_assigned_1
2021-02-24 15:59:13,344 [stats : INFO ] obi stats
99.5 % |#################################################/ ] remain : 00:00:00
SCIENTIFIC_NAME count total
None 184 472601
2021-02-24 15:59:13,456 [stats : INFO ] Done.
Several issues:
- I'm using one sample as a demo which has been demultiplexed, so I didn't use ngsfilter command. Can I skip this if I'm only dealing with one sample?
- I have tried to generate two different databases using different forward primers (trnL g and trnL c, the latter one is what we used in the fluidigm), but I failed for both. Not sure what's going on here and what to solve the problem, but any suggestions would be very helpful!
Thanks.