RuoshiZ
RuoshiZ
Hi, Could you please provide the full log of the two runs? What is the size of your target DB? Are the matches(virus-host pairs) of the rest of the hits...
Hi! The different test files in the example folder came from different bacteria genomes, only the one from fasta_test is supposed to get a hit from one of the example...
Thanks for the reminder and sorry for the delay. Spacedust currently only accepts faa files generated with Prodigal, with which the correct coordinate information can be parsed. If you would...
This should be fixed with 16b0203
Hi! Sorry for the delay. I have found the bug in `gff2db`, but it might take a bit of time to get it fixed, because this module is under MMseqs2....
Hi, I have updated the workflow. Now it is also possible to pass a directory or a .tsv file with the list of paths to the desired files, for example:...
Hi, thanks for your interest! I have created a release: https://github.com/soedinglab/spacedust/releases/tag/1-babc6f8
Hi! PDB100 is a foldseek DB, not a spacedust setDB, which should contain further metadata files like `_member_to_set` needed in the workflow. Unfortunately, PDB100 is not suitable for converting to...
Hi! You are right: Spacedust is able to process fungal genes as long as they are already translated into protein sequences, and the positions should be parsed from the prodigal-like...
Hi! In the paper we removed redundant gene clusters for each query genome, by collapsing/aggregating overlapping query cluster positions regions that hit multiple target gene regions. Please refer to the...