Unexpected BGC Count and error Issues in BiG-SCAPE v2.0.0b6 Analysis

[eeeve-e]

Hello everyone,

I am analyzing a set of BGCs identified using AntiSMASH v7.1.0, consisting of 868 .gbk files. In my last run, I executed the following command:
bigscape cluster -i /userdata2/antiSMASH_7.1.0/antismash_output -o /userdata2/antiSMASH_7.1.0/bigscape2.0/example_output3 -p /userdata2/BiGSCAPE/Pfam-A.hmm --mibig-version 4.0

Based on my results, I have the following questions:

1. When I submitted the example_output3.db result, the interface displayed the following message: An error has occurred: Cannot read properties of undefined (reading ‘count’). What is the cause of this error, and how should I handle it?
2. Why is the total number of BGCs (574) lower than the input count (868)?
3. Regarding genome count, the results indicate only 17 genomes analyzed, but I am working with 157 bacterial genomes (all of them are sequenced in our lab ). Each genome has its own specific name. Is there a recommended approach to address this?

Thanks in advance for your help!

[nlouwen]

Hi!
Thanks for reaching out!

1. Your first question has also recently come up in output database has to be loaded manually in the index.html file #302, likely your NRPS bin only contains "genome" (see answer to question 2/3), which makes the rendering of the heatmap crash. A fix for this is pending for release of beta.8, you can already incorporate this change in your index.html if needed.
2. The pie charts and number of BGCs and genomes shown in the output Input Data section only counts BGCs in the networks, meaning any singleton BGCs (no distances to other BGCs below the used --gcf-cutoffs) are not included. (You could run with --include-singletons to check your numbers)
3. How do you differentiate between genomes? BiG-SCAPE parses the ORGANISM field in the genbank header (see wiki), If this field is not set they will be grouped into an unkown genome.

Let us know if you have any further questions!