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joybio / multiPrime

multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))
MIT License
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Index Error: list index out of range #11

Open yuzh2000 opened 9 months ago

yuzh2000 commented 9 months ago

Hello！I have some errors when running the program, I would be grateful if you could take time out of your busy schedule to answer my doubts.Pic 1:Is it because of the primer dimer in the result, and if so, what parameters can I improve to solve this problem? Pic 2: Is the reason for the error because the amplicon fragment designed by the software for Cluster_18_59 is smaller than the set parameter value? (3) If the desired amplicon size is within 300 ，and the template sequence size is between 300 - 400, will this affect the results? Finally, I would like to express my thanks again！ 1 2

joybio commented 9 months ago

I apologize for the delayed response. I have been investigating the error and identified a potential source. It appears that the error is linked to excessively long FASTA IDs in your file. Ideally, the IDs should not exceed 20 characters in length. To resolve this, you can either manually modify the IDs or update the 'multiPrime' script, specifically the 'seq_format.py'. If you still encountered this question, you can contact me bby wechat or try multiPrime in web server: https://multiprime.cn/

yuzh2000 commented 9 months ago

Thank you very much for your reply letter! I will rework my sequence ID; in the meantime, I have once again encountered a problem, I entered the conserved region sequence of the bacteria, why the same bacteria is divided into multiple clusters, what is the reason for this? I hope you can give me some advice, I would greatly appreciate it! Looking forward to your reply. d82586cef9e0970c2510c3b8a8b20c1

joybio commented 9 months ago

MultiPrime utilizes CD-hit for sequence clustering and merges the clusters based on ANI results. By default, the second step is overlooked, but you can reset the parameters in the multiPrime.yaml file for testing purposes. Additionally, the MultiPrime2-GUI directly processes multi-alignment input without splitting it into clusters.

yuzh2000 commented 9 months ago

Thank you very much for answering my question! Last time I changed my sequence ID, the program worked fine; Thanks again for your help!

guangingmai commented 9 months ago

I encountered the same issue as @yuzh2000, even though I've shortened the ID to less than 20 characters. However, I still get an error after running. What could be the cause of this?" Snipaste_2024-01-24_20-08-44

joybio commented 9 months ago

Dear @guangingmai , To resolve this, you can either manually modify the IDs or update the 'multiPrime' script, specifically the 'seq_format.py'. If you still encountered this question, you can contact me by wechat (Mini-joybio) or try multiPrime in web server: https://multiprime.cn/