Unexpected output - Githubissues

Hi there, I'm running DAS_Tool 1.1.4 (conda) and am not 100% sure how to interpret the error message and output when I run the command:

DAS_Tool -i 0168172199/DAS_Tool/metabat_scaffold2bin.txt,0168172199/DAS_Tool/maxbin_scaffold2bin.txt,0168172199/DAS_Tool/concoct_scaffold2bin.txt -l metabat,maxbin,concoct -c 0168172199/assembly/0168172199.fa -o dastool_out --search_engine diamond --threads 7 --write_bins --write_unbinned

On the command line, I get the following error message, which isn't very informative:

DAS Tool 1.1.4

Analyzing assembly 
Predicting genes 
Annotating single copy genes using diamond 
Dereplicating, aggregating, and scoring bins 
[1] -1
Writing bins 
/gstore/scratch/u/tamburif/MI_2021/MAGs/.snakemake/conda/9ddf7b1836533eb057c35a3b1337d129/share/das_tool-1.1.4-0/src/extract_bins.sh: line 10: dastool_out_DASTool_contig2bin.tsv: No such file or directory
pullseq - failed to open names file dastool_out_DASTool_bins/*.DasToolBin.tmp
rm: cannot remove ‘dastool_out_DASTool_bins/*.DasToolBin.tmp’: No such file or directory

The output log, dastool_out_DASTool.log, is more helpful and indicates that no bins were found that meet the score_threshold:

DAS Tool 1.1.4

2022-03-25 12:12:08 

Parameters: 
--bins  0168172199/DAS_Tool/metabat_scaffold2bin.txt,0168172199/DAS_Tool/maxbin_scaffold2bin.txt,0168172199/DAS_Tool/concoct_scaffold2bin.txt
--contigs   0168172199/assembly/0168172199.fa
--outputbasename    dastool_out
--labels    metabat,maxbin,concoct
--search_engine diamond
--proteins  NULL
--write_bin_evals   FALSE
--write_bins    TRUE
--write_unbinned    TRUE
--threads   7
--score_threshold   0.5
--duplicate_penalty 0.6
--megabin_penalty   0.5
--dbDirectory   db
--resume    FALSE
--debug FALSE
--version   FALSE
--help  FALSE
--create_plots  FALSE

Dependencies: 
prodigal    /gstore/scratch/u/tamburif/MI_2021/MAGs/.snakemake/conda/9ddf7b1836533eb057c35a3b1337d129/bin/prodigal
diamond /gstore/scratch/u/tamburif/MI_2021/MAGs/.snakemake/conda/9ddf7b1836533eb057c35a3b1337d129/bin/diamond
pullseq /gstore/scratch/u/tamburif/MI_2021/MAGs/.snakemake/conda/9ddf7b1836533eb057c35a3b1337d129/bin/pullseq
ruby    /gstore/scratch/u/tamburif/MI_2021/MAGs/.snakemake/conda/9ddf7b1836533eb057c35a3b1337d129/bin/ruby
usearch 
blastp  /gstore/scratch/u/tamburif/MI_2021/MAGs/.snakemake/conda/9ddf7b1836533eb057c35a3b1337d129/bin/blastp

Analyzing assembly 
Predicting genes 
Annotating single copy genes using diamond 
Dereplicating, aggregating, and scoring bins 
No bins with bin-score >0.5 found. Adjust score_threshold to report bins with lower quality.
 Aborting.

Writing bins

DAS_Tool then writes an empty file, *.fa, to the output bins folder (dastool_out_DASTool_bins in this example) which kind of seems like strange behavior, or maybe a bug?

My question/comment: is this the anticipated behavior? Is there a flag that I'm missing to skip writing *.fa when zero bins meet the score_threshold?

Thank you!

cmks / DAS_Tool

Unexpected output #79