dRep failes when no genome passes the filtering step about drep HOT 4 CLOSED

Hi Johannes,

That's really weird...

It seems like this would happen if 1) all your genomes got filtered out, or 2) the *.fna isn't hitting any genomes.

In the data_tables/ folder, there should be a file called Bdb.csv. Does that have any genomes in it?

Additionally, with the above step (the filtering step), does it say something like X genomes passed quality filtering?

-Matt

from drep.

You are right, it seems to be the filtering, though this shouldn't result in an error like this IMO.

***************************************************
    ..:: dRep dereplicate Step 1. Filter ::..
***************************************************
    
Will filter the genome list
Calculating genome info of genomes
50.00% of genomes passed length filtering
Running prodigal
Running checkM
0.00% of genomes passed checkM filtering

Bdb.csv is empty, accordingly. I suppose it's easy to fix and stop after step 1, if now genome passes the filtering. Similarly, I would try to catch an empty list of files in the input to improve the usability.

BTW: What happens, if file names or sequences IDs contain commas, is that escaped in the CSV files? Wouldn't it be better to report using tab-separated TSV files?

Best,
Johannes

from drep.

Hi Johannes,

Thanks for the suggestion- will add to my internal to-do list.

As for the commas, they are current not escaped. You are right that maybe I should have done TSV files from the get-go, but as it would be a pain to change now and because commas in filenames are very rare, I will probably not change it unless it becomes a bigger issue.

Best,
-Matt

from drep.

Hi Matt,

what about leaving bug reports open until they have been addressed in a commit?

PS: I do have commas in many files.

from drep.