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DAS Tool
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Error: DAS Tool #105

Open ramnageena11 opened 1 month ago

ramnageena11 commented 1 month ago

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 -o DAS_Tool -i -c -o [--labels=] [--proteins=] [--threads=] [--search_engine=] [--score_threshold=] [--dbDirectory= ] [--megabin_penalty=] [--duplicate_penalty=] [--max_iter_post_threshold=] [--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= Engine used for single copy ge Execution halted

Quzelei commented 1 month ago

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

ramnageena11 commented 1 month ago

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 commented 1 month ago

Hi, Pls look into the error.

Thanks rgds Ram

ramnageena11 commented 4 weeks ago

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 commented 4 weeks ago

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 commented 4 weeks ago

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 https://github.com/cmks/DAS_Tool/issues/105#issuecomment-2148391368, or unsubscribe https://github.com/notifications/unsubscribe-auth/AK4LETVEWX46OMDNKIWAHD3ZFYR2LAVCNFSM6AAAAABITSJUAKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBYGM4TCMZWHA . You are receiving this because you authored the thread.Message ID: @.***>