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yinlabniu / HGT-Finder

Program for finding horizontal gene transfer using BLAST result
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HGTfinder errror #2

Open gsun2unl opened 5 years ago

gsun2unl commented 5 years ago

Hi, I am currently trying to use HGT finder following the readme file, however, it gave me this error: Invalid R value for subject: 5***

And eventually, the program was halted with this error:

Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are not allowed Calls: qvalue -> pi0est -> smooth.spline

Can you give me some clue on fixing them? Thank you!

Tinyman392 commented 5 years ago

The error stems from the Invalid R value for your subject. More specifically, this message is triggered when the bit score of the query to itself is lower than the bit score between the query and the subject (which theoretically shouldn't happen, but can in practice). We've seen this occur with sequences that contain N (wildcard) values.

Off the top of my head I do not remember if the message is more likely to be triggered if the query has many N characters or if it's the subject. You'd need to check both and possibly exclude that (those) sequence(s) from the analysis.

The Error in the qvalue (smooth.spline) call is triggered most likely due to having an invalid P-value due to the invalid R value.