sortmerna command not working

Question

[Shahzad]

Dear All

I need some help. I am getting an error in running sortmerna tool. I have successfully indexed the reference rRNA database.

Command used for indexing db:

./indexdb_rna --ref ./rRNA_databases/silva-euk-28s-id98.fasta,./index/silva-euk-28s-db -v

It made 4 files in the index folder named

silva-euk-28s-db.bursttrie_0.dat  
silva-euk-28s-db.kmer_0.dat  
silva-euk-28s-db.pos_0.dat  
silva-euk-28s-db.stats

Next step is to filter RNA-seq reads from rRNA indexed database. The command used for this was:

./sortmerna --ref '/home/laptop/Desktop/NGS_tools/sortmerna-2.1/rRNA_databases','/home/laptop/Desktop/NGS_tools/sortmerna-2.1/index' --reads '/home/laptop/Desktop/RNA-seq/subdir1/output.fastq' --aligned sortmeout --fastx --other RNAsortme --log

This is resulting in following error

ERROR: The index '/home/laptop/Desktop/NGS_tools/sortmerna-2.1/index.stats' does not exist.
  Make sure you have constructed your index using the command `indexdb'. See `indexdb -h' for help.

Please help if you notice that I did something wrong here.

[5heikki]

I don't know the tool, but having glimpsed at the manual, should you not define a fasta file as a reference to the sortmerna tool (instead of just some folder like in your command)? Likewise, it looks to me like you're not defining the location of the index file correctly (also in error message). Shouldn't it be:

./sortmerna --ref /home/laptop/Desktop/NGS_tools/sortmerna-2.1/rRNA_databases/silva-euk-28s-id98.fasta,/home/laptop/Desktop/NGS_tools/sortmerna-2.1/index/silva-euk-28s-db --reads ..etc

[Shahzad]

Thank you @5heikki It solved my problem. Regards.