RNAfold is OK but RNAduplex cannot be executed in miRdup process
Hello,
I got an issue regarding miRdup execution when I execute it RNAfold seems to work well but the problem rather comes from subsequent RNAduplex processing. (OS : W10). I'm beginner and I'm not really used to all this but maybe the whole problem comes from Windows?
I paste RNAfold, RNAduplex and .dll in miRdup folder, I also tried to execute from Vienna Tool folder directly. My infiles are in fasta.
cl = ['java','-jar','miRdup_1.4/miRdup.jar','-predict','-i', 'output1/pre_seq_map.fasta','-m', 'output1/miRNA_map.fasta', '-r','miRdup_1.4']
subprocess.call(cl) #also tried directly on windows command line
____________________________
checking RNAfold... OK
**checking RNAduplex... FAIL**
Vienna tools cannot be executed
Process finished with exit code 0
____________________________
ls miRdup_1.4
.local
lib
libgcc_s_seh-1.dll
libgomp-1.dll
libgsl-0.dll
libgslcblas-0.dll
libwinpthread-1.dll
miRdup.jar
readme.txt
RNAduplex.exe
RNAfold.exe
src
testFiles
So I'm wondering why is this happening. Thank you
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Ram
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beauchemin.david.3 •
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beauchemin.david.3 •
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You put RNAfold.exe, RNAduplex.exe and dlls in miRdup folder, good, but you should execute the command within the folder itself.
java -jar miRdup.jar -predict -i output1/pre_seq_map.fasta -m output1/miRNA_map.fasta
-r option is not recognized on windows
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mickael.leclercq •
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I assume you have taken this note for Windows into consideration?
Changing PATH in Windows.
Edit: Are you running this directly in windows or in cygwin/unix environment?
I did it yes
I run it directly on windows 10 I should figure out to change environment..