search

GiantSpaceRobot / FindFungi

A pipeline for the identification of fungi in public metagenomics datasets
16 stars 15 forks source link

assembly_data #11

Closed tsoratto closed 3 years ago

tsoratto commented 4 years ago

Hi!

I'm trying to adapt the pipeline to run it with an assembly data. I changed the cut-off of 10 reads predicted per species, but I'm not sure if the blastn is running. I got this message: image Do you know if the blastn is running and I don't have any match? Or if is it not running?

thank you for the attencion!

GiantSpaceRobot commented 4 years ago

Hi there,

I am not sure what you mean regarding assembly data. Nevertheless, the pipeline should work for any FASTQ data.

As for your problem, it looks as though blastn is not running correctly due to the query files being empty. Does the directory 'Processing/' contain files named 'ReadNames_bsub.TAXID.fsa'? For example, the file 'ReadNames_bsub.5421.fsa' should be in that directory.

If these files exist, do they contain the read sequences?