Error while running VF.pred on my own data

[raquelnb]

Error while running VF.pred on my own data

[raquelnb]

The command that i used was:

inFaFile <- system.file("data","A04_SED_spades_contig_300.fasta",package="VirFinder")
predResult <- VF.pred(inFaFile)

[jessieren]

Hi raquelnb,

Thanks for using VirFinder. I am not sure what the problem is from the error message. It seems like some data formatting issue but I cannot confirm. Do you mind attaching a small test example so that I can try to take a look on my side?

Thank you!

Jessie

[raquelnb]

Of course Jie, here it is.
test.txt

Thank you!

[jessieren]

Hi raquelnb,

I tested the file on my computer (MacOS) and it runs well. The results are as follows,

VF.pred("/Users/jessie/Library/Containers/com.apple.TextEdit/Data/Desktop/test.txt")
[1] "test.txt [1] line1-3 NODE_6501_length_3412_cov_6.880060_magnitude=599 len 3412 score 0.0067 pvalue 0.7795"
[1] "test.txt [2] line3-5 NODE_6502_length_3412_cov_4.940330_magnitude=452 len 3412 score 0.1844 pvalue 0.2367"
[1] "test.txt [3] line5-7 NODE_6503_length_3411_cov_15.362328_magnitude=1251 len 3411 score 6e-04 pvalue 0.9602"
[1] "test.txt [4] line7-9 NODE_6504_length_3411_cov_11.642771_magnitude=794 len 3411 score 0.0278 pvalue 0.5595"
[1] "test.txt [5] line9-11 NODE_6505_length_3411_cov_7.175465_magnitude=529 len 3411 score 0.0098 pvalue 0.7263"
[1] "test.txt [6] line11-13 NODE_6506_length_3411_cov_5.165567_magnitude=598 len 3411 score 0.1908 pvalue 0.2317"
[1] "test.txt [7] line13-15 NODE_6507_length_3411_cov_4.211458_magnitude=277 len 3411 score 0.1512 pvalue 0.2676"
[1] "test.txt [8] line15-17 NODE_6508_length_3411_cov_3.177265_magnitude=199 len 3411 score 0.0076 pvalue 0.7639"
[1] "test.txt [9] line17-18 NODE_6509_length_3411_cov_2.847331_magnitude=224 len 3411 score 0.5724 pvalue 0.0718"
name length score
1 NODE_6501_length_3412_cov_6.880060_magnitude=599 3412 0.0067461441
2 NODE_6502_length_3412_cov_4.940330_magnitude=452 3412 0.1843632302
3 NODE_6503_length_3411_cov_15.362328_magnitude=1251 3411 0.0006201783
4 NODE_6504_length_3411_cov_11.642771_magnitude=794 3411 0.0277882418
5 NODE_6505_length_3411_cov_7.175465_magnitude=529 3411 0.0098366301
6 NODE_6506_length_3411_cov_5.165567_magnitude=598 3411 0.1908007627
7 NODE_6507_length_3411_cov_4.211458_magnitude=277 3411 0.1511859759
8 NODE_6508_length_3411_cov_3.177265_magnitude=199 3411 0.0076277105
9 NODE_6509_length_3411_cov_2.847331_magnitude=224 3411 0.5723540036
pvalue
1 0.77952947
2 0.23672083
3 0.96022314
4 0.55954402
5 0.72629154
6 0.23174873
7 0.26764492
8 0.76388552
9 0.07179238

So I am not sure what was the problem on your side...