Comments (4)
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.
Related Issues (20)
- Inquiry on Optimal Workflow for Metagenomic Binning and Dereplication HOT 2
- Drep error with fastANI HOT 1
- Drep error with fastANI HOT 2
- Steps to implement checkm2 quality report to dRep HOT 8
- Halt: the pair-wise MASH clustering step HOT 5
- extra_weight_table flag HOT 3
- Issue with ANImf: 0% ANI despite similar nucleotide sequences HOT 11
- Is there any plan to add skani as ANI calculation method? HOT 2
- drep stoped during clustering HOT 9
- drep conda installation dependencies HOT 4
- dRep: Argument list too long HOT 3
- stuck on checkm HOT 1
- Question abunt the output of dRep HOT 1
- file exists but get os.path.isfile(genome), "{0} is not a file".format(genome) error HOT 10
- ValueError: mash isn't working- make sure its installed HOT 2
- checkM overwriting itself? HOT 4
- checkM failed, properly related HMM file HOT 1
- Contrast of text in dendograms HOT 1
- assert os.path.isfile(genome), "{0} is not a file".format(genome) AssertionError: ......./b1.fasta is not a file HOT 2
- Singularity image
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