empty out and readb folders

[mdsufz]

Hi, I am using sortmerna to calculate coverage and abundance of reads from rRNA predictions (using MATAM) on the metagenomic libraries. However, the folders out and readb are always empty. Any reason why this is happening?

[ppericard]

Hi @mdsufz, Could you explain to us in a bit more detail what you're trying to do? Are you trying to align reads using SortMeRNA (which version ?) on a custom reference database of MATAM-reconstructed rRNA full-length sequences? Can you give us an example of the command line you're running ? Thanks in advance Pierre

[mdsufz]

Hi Pierre,

yes, we are trying to align the predicted 16S sequences (from MATAM) to the libraries from which they originated. I am currently using SortMeRNA version 4.3.6.

an example of the command line is as follows:

sortmerna --ref sample_library.fasta --reads bac_ssu_reps_97.fasta --otu_map TRUE --workdir output_folder

bac_ssu_reps_97.fasta = predicted 16S sequences sample_library.fasta = metagenomic library

Best regards,

Joao On 18/04/23 12:24, Pierre Pericard @.***> wrote:

Hi @mdsufz(https://github.com/mdsufz ), Could you explain to us in a bit more detail what you're trying to do? Are you trying to align reads using SortMeRNA (which version ?) on a custom reference database of MATAM-reconstructed rRNA full-length sequences? Can you give us an example of the command line you're running ? Thanks in advance Pierre

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[biocodz]

can you provide the execution trace?