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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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No result for aligned fasta file #12

Open guangingmai opened 9 months ago

guangingmai commented 9 months ago

Hello, I ran the following code, and there were no errors during the execution. However, the resulting file is empty. Why could this be? code: python scripts/multiPrime-core.py -i workspace/inputs/MICrhoDE_dna_aligned.msa -o workspace/res/PR_out -p 8 -l 24 -n 4 -d 10 -v 1 -e 3.6 -g 0.4,0.6 -f 0.8 -c 4 -a 4 MICrhoDE_dna_aligned.txt Please change the file extension from txt to msa

joybio commented 9 months ago

The alignment file exhibits suboptimal quality; consider adjusting parameters such as -g 0.1,0.9 and -f 0.1. However, obtaining satisfactory results may be challenging due to the poor quality of the multialignment. Additionally, your fasta file appears to be too short, and the conserved region is inadequately small. It might be worth exploring the use of multiPrime2-GUI to search for potential primer candidates, although I cannot assure optimal results.

joybio commented 9 months ago

Dear @guangingmai , I regret to inform you that I have attempted to utilize your input file with multiPrime2-GUI, but unfortunately, it has proven unsuccessful. The challenging quality of the multiple alignment file continues to pose difficulties for the primer design process. If there are alternative approaches or additional information that could enhance the alignment quality, please provide them so we can explore other avenues for a successful outcome.