-
Notifications
You must be signed in to change notification settings - Fork 17
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
DAS Tool not generating refined bin files #93
Comments
Hi @rialc13, Technically, you are right and an "unbinned.fa" file could be generated in this case containing all contigs of the input fasta file. |
Hi @cmks, |
Hi @cmks, I'm getting the same error despite having version 1.1.6. Are there some mandatory options to avoid getting this error? Best regards |
Hi. I am running the DAS Tool with the --score_threshold 0.4 and it is unable to generate refined bin files. In the bins folder, it is reporting a single file called *.fa which is a blank file. In case binning is not taking place, shouldn't atleast an unbinned.fa file be reported? And is there any way that the blank *.fa file still have the output base name as mentioned while running the command? Here is the log file -
DAS Tool 1.1.4
2023-01-30 03:57:38
Parameters:
--bins MEGAHIT-MaxBin2-ERR2538413.tsv
--contigs MEGAHIT-ERR2538413.contigs.fa
--outputbasename MEGAHIT-DASTool-ERR2538413
--labels NULL
--search_engine diamond
--proteins NULL
--write_bin_evals TRUE
--write_bins TRUE
--write_unbinned TRUE
--threads 2
--score_threshold 0.4
--duplicate_penalty 0.6
--megabin_penalty 0.5
--dbDirectory db
--resume FALSE
--debug FALSE
--version FALSE
--help FALSE
--create_plots FALSE
Dependencies:
prodigal /usr/local/bin/prodigal
diamond /usr/local/bin/diamond
pullseq /usr/local/bin/pullseq
ruby /usr/local/bin/ruby
usearch
blastp /usr/local/bin/blastp
Analyzing assembly
Predicting genes
Annotating single copy genes using diamond
Dereplicating, aggregating, and scoring bins
No bins with bin-score >0.4 found. Adjust score_threshold to report bins with lower quality.
Aborting.
Writing bins
The text was updated successfully, but these errors were encountered: