SILVA rRNA database

[Hoi Tong]

Hi,

I want to run my paired end sequences against the rRNA database, so I downloaded the SILVA rRNA database with this command: 

• $ kneaddata_database --download ribosomal_RNA bowtie2 $DIR

After downloading, the outputs I got were: 

SILVA_128_LSUParc_SSUParc_ribosomal_RNA.tar.gz

SILVA_128_LSUParc_SSUParc_ribosomal_RNA.rev.2.bt2l

SILVA_128_LSUParc_SSUParc_ribosomal_RNA.rev.1.bt2l

SILVA_128_LSUParc_SSUParc_ribosomal_RNA.4.bt2l

SILVA_128_LSUParc_SSUParc_ribosomal_RNA.3.bt2l

SILVA_128_LSUParc_SSUParc_ribosomal_RNA.2.bt2l

SILVA_128_LSUParc_SSUParc_ribosomal_RNA.1.bt2l

Are these the correct output files? 

Do I have to put my input "db" as all of these files or specific ones? 

I've tried running it on one rRNA file: 

-db SILVA_128_LSUParc_SSUParc_ribosomal_RNA.1.bt2l

but all my outputs have been empty files labeled as:

SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_clean_1.fastq

SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_clean_2.fastq

SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_contam_1.fastq

SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_contam_2.fastq

What is the problem? 

Thanks!

[Andy Shi]

Hi,

You need to specify the base name for all the reference database files. In your case, you should use

-db SILVA_128_LSUParc_SSUParc_ribosomal_RNA