Error while running SNVBOX tool
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2.4 years ago
LimMo ▴ 10

Hi all,

I have a problem regarding running and using SNVBOX database, I'm interested in using the features that have been generated for CHASMplus from SNVBOX.

But the problem is when I'm trying to run the code with this command:

./snvGetTranscript –f featurelist –o outputfilename.arff mutationlist


with my own files, like this:

./snvGetGenomic –f features.lst –o outputfilename.arff mutations.lst


but it keeps giving me this error (it seems that it couldn't see the parameters):

snvGetGenomic: error: Please specify feature file using -f and output file using -o


I tried to investigate their code and print argument when the code tried to pare it but it prints None (it should print the names of the feature and output files).

I double-checked my feature and mutations files and they look good as you can see:

features.lst

AABLOSUM
AACharge
AACOSMIC


And this mutations,lst:

chr1       35416   35416    -     A       G
chr1       54844   54844    +     G       A
chr1       69224   69224    +     A       C
chr1       69230   69230    +     A       C
chr1       69236   69236    +     A       C
chr1       69270   69270    +     A       G


Any help will be appreciated.

chasmplus • 410 views
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Is your file named mutations.lst or mutaions.lst?

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It's mutations.lst, just a typo while writing a question (not in the actual running command). Now I edit the question.