CLARK-l output

[Anthony Messer]

Good Afternoon,

Some assistance would be gratefully received regarding the output from CLARK-l.

I have installed the newest release of CLARK v 1.2.3.1 and downloaded the bacteria database using the ./set_targets command.  However when I run CLARK-l on a small metagenomic test dataset the output is a numerical identifier (shown below) in the assignment column where I was expecting the scientific taxon name.  Do I have to manually translate this number ID (and if so what does this number refer to?) or is there an issue with my download of database or install of CLARK?

Object_ID, Length, Assignment
r1.1,300,2147
r2.1,300,2147
r3.1,300,2147

Thanks in advance for any help,
Anthony

[Rachid]

Hello Anthony !

Thank you for your interest! The output of the results file produced by CLARK-l or any other variant of CLARK is detailed in the README file, please feel free to consult it.

Thus, the third column you refer to is the NCBI taxonomic ID. Then, for example, you can use the script "estimate_abundance.sh" to have detailed taxonomic information (with scientific name, lineage, etc.) of you results.

Cheers,

Rachid