No refined.out and No bin surpasses the cutoff of: 16 when running example

[FengqingWang0712]

Hello there,
Thank you for your great tool.
I met the issue when running the example:Loading packages...
Bisco iteration: 1
Processing candidate bin 48 of 48
Bisco iteration: 2
Processing candidate bin 55 of 55
There were 50 or more warnings (use warnings() to see the first 50)
Refining bins, iteration: 1
Extracting SCG information for bins...
Scores for all initial bins written to: MAGScoT.scores.out
No bin surpasses the cutoff of: 16
Warning message:
In left_join(contig_to_bin.remain %>% filter(contig %in% gene_to_contig$contig), :
Detected an unexpected many-to-many relationship between x and y.
ℹ Row 2 of x matches multiple rows in y.
ℹ Row 164 of y matches multiple rows in x.
ℹ If a many-to-many relationship is expected, set relationship = "many-to-many" to silence this warning.
No bins with score >= 16 were found in the dataset.

I got the same issue when I used my own data.

However, it's successful when I used the S21.contigs_to_bin_R_change5.tsv and S21.hmm file from 'dplyr error in R script #6'.
Can you help me figure it out? Thank you in advance!

Best,

[eikematthias]

Hi, could you please send us your inputs that caused this error? From just the error message, I can only guess that either your inputs may not be properly delimted or your inputs may contain non-unique IDs.

[FengqingWang0712]

Thank you for your reply. Here I attached the hmm and contig_to_bin files.
files.tar.gz

[mruehlemann]

Dear @FengqingWang0712 ,
I downloaded your files and ran MAGScoT with default values:
Rscript MAGScoT.R -i files/new.all.bins.tsv --hmm files/contigs.hmm -o out
without any problem.

One thing that occurs to me, is that your iterations start with 48 and 55 candidates, for me it is 224 and 192 using your files:

Aditionally, your error message states "No bin surpasses the cutoff of: 16", this cutoff for the scoring should be between 0 and 1. Did you set any of the scoring options when starting the script?