DAS_Tool doesn't run at all

[amankowski]

Hi, I installed DAS_Tool and also successfully ran it on the example data. However, when I try to run it on my own dataset, the only thing that happens is that the help message gets printed to my screen. I am thankful for any advice what might be the problem and how to solve this issue.

Here's also the command I am trying to run + the output:

[Fri Jun 07][13:17:52][mankowski@gc-node-1][~/mankowski/symbiosis/gutless/data/metagenomes/2699/2699_A/binning/dastool]
$ DAS_Tool -i fastg_scaffolds2bin.tsv,metabat_scaffolds2bin.tsv -l fastg,metabat -c /opt/extern/bremen/symbiosis/gutless/data/metagenomes/2699/2699_A/spades-k127/contigs.fasta -o ./test

DAS Tool version 1.1.1

Usage: DAS_Tool -i methodA.scaffolds2bin,...,methodN.scaffolds2bin
                -l methodA,...,methodN -c contigs.fa -o myOutput

   -i, --bins                 Comma separated list of tab separated scaffolds to bin tables.
   -c, --contigs              Contigs in fasta format.
   -o, --outputbasename       Basename of output files.
   -l, --labels               Comma separated list of binning prediction names. (optional)
   --search_engine            Engine used for single copy gene identification [blast/diamond/usearch].
                              (default: usearch)
   --write_bin_evals          Write evaluation for each input bin set [0/1]. (default: 1)
   --create_plots             Create binning performance plots [0/1]. (default: 1)
   --write_bins               Export bins as fasta files  [0/1]. (default: 0)
   --write_unbinned           Export unbinned contigs as fasta file. Only has an effect when write_bins==1 [0/1]. (default: 0)
   --proteins                 Predicted proteins in prodigal fasta format (>scaffoldID_geneNo).
                              Gene prediction step will be skipped if given. (optional)
   -t, --threads              Number of threads to use. (default: 1)
   --score_threshold          Score threshold until selection algorithm will keep selecting bins [0..1].
                              (default: 0.5)
   --duplicate_penalty        Penalty for duplicate single copy genes per bin (weight b).
                              Only change if you know what you're doing. [0..3]
                              (default: 0.6)
   --megabin_penalty          Penalty for megabins (weight c). Only change if you know what you're doing. [0..3]
                              (default: 0.5)
   --db_directory             Directory of single copy gene database. (default: install_dir/db)
   --resume                   Use existing predicted single copy gene files from a previous run [0/1]. (default: 0)
   --debug                    Write debug information to log file.
   -v, --version              Print version number and exit.
   -h, --help                 Show this message.

Example 1: Run DAS Tool on binning predictions of MetaBAT, MaxBin, CONCOCT and tetraESOMs. Output files will start with the prefix DASToolRun1: 
   DAS_Tool -i sample_data/sample.human.gut_concoct_scaffolds2bin.tsv,sample_data/sample.human.gut_maxbin2_scaffolds2bin.tsv,sample_data/sample.human.gut_metabat_scaffolds2bin.tsv,sample_data/sample.human.gut_tetraESOM_scaffolds2bin.tsv -l concoct,maxbin,metabat,tetraESOM -c sample_data/sample.human.gut_contigs.fa -o sample_output/DASToolRun1

Example 2:  Run DAS Tool again with different parameters. Use the proteins predicted in Example 1 to skip the gene prediction step. Set the number of threads to 2 and score threshold to 0.1. Output files will start with the prefix DASToolRun2: 
   DAS_Tool -i sample_data/sample.human.gut_concoct_scaffolds2bin.tsv,sample_data/sample.human.gut_maxbin2_scaffolds2bin.tsv,sample_data/sample.human.gut_metabat_scaffolds2bin.tsv,sample_data/sample.human.gut_tetraESOM_scaffolds2bin.tsv -l concoct,maxbin,metabat,tetraESOM -c sample_data/sample.human.gut_contigs.fa -o sample_output/DASToolRun2 --threads 2 --score_threshold 0.6 --proteins sample_output/DASToolRun1_proteins.faa

Please cite: Sieber et al., 2018, Nature Microbiology (https://doi.org/10.1038/s41564-018-0171-1).

Best, Anna

[cmks]

Sorry, I can't replicate your problem. I used your exact same command (with different file contents) and DAS Tool is running for me. The help page should only appear if your syntax is incorrect (or if you type --help). The fact that you can run DAS Tool on the example data means that your installation is good.

[susheelbhanu]

Hey Anna,

I was having the exact same problem as you. Below is how I was trying to run DAS_Tool.

DAS_Tool  -i maxbin2.scaffolds2bin.tsv, metabat2.scaffolds2bin.tsv \
               -l maxbin2,metabat2 \
               -c /scratch/users/sbusi/extraction_methods/fastq_NewZealand/B12_filtered_megahit/final.contigs.fa \
               -o B12_dastool_output/DASToolRun1 \
                 --search_engine diamond \
                 --write_bin_evals 1 \
                 --write_bins 1 \
                 --threads 24 \
                 --db_directory /home/users/sbusi/apps/DAS_Tool-master/db \
                 --create_plots 1

However, this only gave me the help screen every single time.

When I tried to re-run it without breaking the code into new lines, it seemed to have worked.

DAS_Tool -i maxbin2.scaffolds2bin.tsv,metabat2.scaffolds2bin.tsv -c ../B4_filtered_megahit/final.contigs.fa -o B4_dastool_output --search_engine diamond -l maxbin2,metabat2 --write_bins 1 --write_bin_evals 1 --threads 23 --db_directory /home/users/sbusi/apps/DAS_Tool-master/db/ --create_plots 1

Good luck, Susheel

[cmks]

Thanks for sharing @susheelbhanu! @amankowski did you figure out what the problem was in your case? What type of shell and operating system are you using?

[valzip]

Hi @cmks I have similar problem using Ubuntu 20.04 LTS and bash. I tried DAS Tool version 1.1.2. Command is in single line, and it still ends in "help" output. DAS_Tool -i concoct.scaffolds2bin.tsv,metabat.scaffolds2bin.tsv,maxbin.scaffolds2bin.tsv -l concoct,metabat,maxbin -c A01_megahit_over1000_cured.fasta -t 8 --write_bins 1 --proteins -o DAS_Tool_output/DASToolRun1

[amankowski]

Hi everyone, thanks to replying to my problem. I finally got DASTool to run (without really knowing how, to be honest): for me it started working when I used the results of three different binning tools instead of just two, which I have done previously. I don't know how this solved the problem or what else changed but at least I got my desired results. Cheers, Anna