Error: DAS Tool

[ramnageena11]

Hi,
I am running DAS Tool on conda environment. Not able to figure out what is the issue and how to resolve.

I am getting this error:
DAS_Tool -i concoct_contigs2bin.tsv,maxbin_contigs2bin.tsv,metabat_contigs2bin.tsv -l concoct,maxbin,metabat -c /media/majorram/Analysis_Data/singhrn/meta_assembly/assembly_all/medaka_polis/meda_polis_con-assembly/meda_all_consen.fasta -o /media/majorram/Analysis_Data/singhrn/meta_assembly/binning/dasTool/dasTool-results/dasT --search_engine diamond --proteins /media/majorram/Analysis_Data/singhrn/meta_assembly/binning/dasTool/dasTool-results/dasT-proteins.faa --write_bins --write_bin_evals --create_plots --threads 30
Error: DAS Tool

Usage:
DAS_Tool [options] -i -c <contigs_fasta> -o
DAS_Tool -i -c <contigs_fasta> -o [--labels=] [--proteins=<proteins_fasta>] [--threads=] [--search_engine=<search_engine>] [--score_threshold=<score_threshold>] [--dbDirectory= ] [--megabin_penalty=<megabin_penalty>] [--duplicate_penalty=<duplicate_penalty>] [--max_iter_post_threshold=<max_iter>] [--write_bin_evals] [--write_bins] [--write_unbinned] [--resume] [--debug]
DAS_Tool [--version]
DAS_Tool [--help]

Options:
-i --bins= Comma separated list of tab separated contigs to bin tables.
-c --contigs= Contigs in fasta format.
-o --outputbasename= Basename of output files.
-l --labels= Comma separated list of binning prediction names.
--search_engine=<search_engine> Engine used for single copy ge
Execution halted

[Quzelei]

Hi, I have the same error as yours. Did you finally solved it？

[ramnageena11]

Hi, No, unfortunately, I am not able to figure out what the issue is. It does not mention the error.
Have you able to resolve it?

[ramnageena11]

Hi,
Pls look into the error.

Thanks
rgds
Ram

[ramnageena11]

Hi, I have the same error as yours. Did you finally solved it？

Hi,
I created separate environment in conda and run following command and it worked.

DAS_Tool -i concoct_contigs2bin.tsv,maxbin_contigs2bin.tsv,metabat_contigs2bin.tsv -c /consen.fasta -o dasTool-results/dasT -l concoct,maxbin,metabat --search_engine diamond --write_bin_evals --write_bins --write_unbinned -t 30

[cmks]

Double check your command. --create_plots is not a valid option. Unfortunately, typos in the command line are not reported due to a bug in the docopt R package.

[ramnageena11]

Hi, How to create plots/ graphs and visualize results? Thanks Ram Ram Nageena Singh, Ph.D (

…

On Tue, Jun 4, 2024 at 14:48 cmks ***@***.***> wrote: Double check your command. --create_plots is not a valid option. Unfortunately, typos in the command line are not reported due to a bug <https://github.com/cmks/DAS_Tool?tab=readme-ov-file#docopt-issue> in the docopt R package. — Reply to this email directly, view it on GitHub <#105 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AK4LETVEWX46OMDNKIWAHD3ZFYR2LAVCNFSM6AAAAABITSJUAKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBYGM4TCMZWHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[jadeaver]

In case any one else is still getting this error, I was also getting this error. I ended up putting quotations around my input files (like below) and it worked for me. For example:

-i"concoct_contigs2bin.tsv","maxbin2_contigs2bin.tsv"`