How to generate a cluster file for identifying recombinants in all SARS-CoV-2 sequences

[hyzhou1990]

Hi, Dr. Varabyou. I am a researcher from China. Thank you for your efforts in developing bolotie, which has undoubtedly accelerated the advancement of the field.

Since the identification of XBB lineages, there has been increasing attention on recombinants of SARS-CoV-2. We are interested in applying bolotie to analyze all 14,000,000 sequences and identify as many recombinants as possible.

However, when we generated a cluster file and ran a test program, we did not achieve the expected results. Here were our cluster file, input file and the logs.
Attached_log_clus.zip

[hyzhou1990]

I have tried the problem matrix in the ftp server and got the information below.

[alevar]

Hi!

Thank you for looking into using our software! I am very intrigued by the prospects of testing it on 14,000,000 genomes and learning about the results! Unfortunately, I will be away and unable to check your issue until next Tuesday. I hope this slight delay will not hinder your study. I will follow up in this thread as soon as I'm back and able to take a look at it!

Thank you,

Ales

[hyzhou1990]

Thank you for your reply. I appreciate your interest in this proposal, and I will patiently wait for your response when you're back.