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broadinstitute / adapt

A package for designing activity-informed nucleic acid diagnostics for viruses.
MIT License
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Error when trying to run complete-targets #73

Open buchanri opened 2 months ago

buchanri commented 2 months ago

Hello, I'm new to bioinformatics and I'm trying to run this command using your program

_design.py complete-targets fasta /nfs7/BPP/Chang_Lab/buchanri/agro_crispr_dx/data/fna_assemblies/B133-95_BV2_NA_T1a.fna --obj maximize-activity -gl 28 -pl 30 -pm 1 -pp 0.95 --predict-cas13a-activity-model -o /nfs7/BPP/Chang_Lab/buchanri/agro_crispr_dx/results/adaptBV/trial1

But I keeping getting error of ValueError: Sequences must be the same length. What does this mean and how do I fix it? I've tried using no parameters to keep it simple too but I still get the same error. Thanks!

haydenm commented 2 months ago

I believe you are seeing that error because when using the fasta mode ADAPT will, by default, assume that your input sequences are aligned. If your sequences are aligned, they should all be the same length. If they are unaligned, you should pass the arguments --unaligned and --mafft-path. ADAPT will then align them for you. See this part of the README for more details.