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jessieren / VirFinder

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
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VirFinder application in transcriptomes #13

Open denisbruno1 opened 5 years ago

denisbruno1 commented 5 years ago

Hello, Jessieren!

I`m trying to run VirFinder 1.1 in Ubuntu to discover viruses in transcriptomes. Methodology of the package is able to detect this? The following error occurs when I tried to do that

Error in countSeqFeatureCpp(seqFa, w) : Not compatible with STRSXP: [type=NULL]. In addition: Warning message: In file(inFaFile, open = "r") : file("") only supports open = "w+" and open = "w+b": using the former

Can you help with that, please? Cheers

jessieren commented 5 years ago

Hi denisbruno,

Did you solve the problem? If not, could you please send me the command you use? Thanks!

(sorry that I thought I replied your message through emails, but seems not).

Jessie

miasungeunlee commented 5 years ago

Dear Jessie, Same problem with denisbruno; Here is the command what i used.

Test run with crAssphage.fasta worked but with my test.fasta file, it doesn't work.

inFaFile <- system.file("data", "crAssphage.fasta", package="VirFinder") VF.pred(inFaFile) [1] "crAssphage.fasta [1] line1-1389 gi|674660337|ref|NC_024711.1| Uncultured phage crAssphage, complete genome len 97065 score 0.9826 pvalue 0.0034" name 1 gi|674660337|ref|NC_024711.1| Uncultured phage crAssphage, complete genome length score pvalue 1 97065 0.982621 0.003395586 inFaFile <- system.file("data", "test.fasta", package="VirFinder") predResult <- VF.pred(inFaFile) Error in countSeqFeatureCpp(seqFa, w) : Not compatible with STRSXP: [type=NULL]. De plus : Warning message: In file(inFaFile, open = "r") : file("") accepte seulement open = "w+" et open = "w+b" : utilisation du premier

Thanks Best wishes LEE

raquelnb commented 4 years ago

I had the same problem!

raquelnb commented 4 years ago

Did you guys got the way to solve it? Thank you!

miasungeunlee commented 4 years ago

Hello, I solved a problem using DeepVIrFinder but still have some problem for predicting q-value from p-value. Waiting her comment on https://github.com/jessieren/DeepVirFinder/issues/6 Try this program, it is more recent. If it works to you, let me know please :D

Mia

raquelnb commented 4 years ago

Oh thank you Mia! I'm going to try it out, I'll let you know. Best

miasungeunlee commented 4 years ago

I re-verified, it worked fine for me too !