mirDup. MicroRNA prediction. java Error software [solved]

Question

[margxenscienculo]

Good morning.

I am using your software mirDup. I cant make the first step. I mean that the java isnt work. I wonder if it is my fault or it is this mirDup software. I attach my error prompt.

Thanks in advance

$ /usr/bin/java -Xms500m -Xmx1500m -jar miRdup.jar -r /home/soba/Ensambladores/ViennaRNA-1.8.5/Progs/ 

java.io.IOException: Cannot run program "/home/soba/Ensambladores/ViennaRNA-1.8.5/Progs/RNAfold": error=2, There is no such file or directory at java.lang.ProcessBuilder.start(ProcessBuilder.java:1041) at java.lang.Runtime.exec(Runtime.java:617) at java.lang.Runtime.exec(Runtime.java:450) at java.lang.Runtime.exec(Runtime.java:347) at miRdup.Vienna.GetSecondaryStructure(Vienna.java:137) at miRdup.Vienna.checkViennaTools(Vienna.java:368) at miRdup.Main.main(Main.java:124) Caused by: java.io.IOException: error=2, No existe el fichero o el directorio at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.<init>(UNIXProcess.java:135) at java.lang.ProcessImpl.start(ProcessImpl.java:130) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1022) ... 6 more checking RNAfold... FAIL Vienna tools cannot be executed

[Martombo]

you see in the last two lines that the problem is about RNAfold, a program of the Vienna tools. do you have it on your computer? if not you can download it from http://www.tbi.univie.ac.at/RNA/

[margxenscienculo]

I had downloaded it. v 1.8.5 and v 2.1.7. Nothing version works.

[Pierre Lindenbaum]

show us the ouput of `ls -la /home/soba/Ensambladores/ViennaRNA-1.8.5/Progs/RNAfold`

[margxenscienculo]

ls -la
total 220
drwxrwxrwx  2 soba soba  4096 feb 28  2011 .
drwxrwxrwx 12 soba soba  4096 feb 28  2011 ..
-rwxrwxrwx  1 soba soba   233 jun 29  2009 Makefile.am
-rwxrwxrwx  1 soba soba 20342 mar 31  2010 Makefile.in
-rwxrwxrwx  1 soba soba  4018 feb 23  2009 RNAaliduplex.c
-rwxrwxrwx  1 soba soba 17123 jun 20  2009 RNAalifold.c
-rwxrwxrwx  1 soba soba 17460 sep  3  2009 RNAcofold.c
-rwxrwxrwx  1 soba soba 12003 feb 23  2009 RNAdistance.c
-rwxrwxrwx  1 soba soba  5024 feb 23  2009 RNAduplex.c
-rwxrwxrwx  1 soba soba  5515 feb 23  2009 RNAeval.c
-rwxrwxrwx  1 soba soba  9481 feb 22  2010 RNAfold.c
-rwxrwxrwx  1 soba soba  6157 feb 23  2009 RNAheat.c
-rwxrwxrwx  1 soba soba  5880 feb 23  2009 RNAinverse.c
-rwxrwxrwx  1 soba soba  6279 feb 23  2009 RNALfold.c
-rwxrwxrwx  1 soba soba  8034 feb 23  2009 RNApaln.c
-rwxrwxrwx  1 soba soba  6819 feb 23  2009 RNApdist.c
-rwxrwxrwx  1 soba soba 10594 jul  8  2010 RNAplfold.c
-rwxrwxrwx  1 soba soba  3132 sep  9  2009 RNAplot.c
-rwxrwxrwx  1 soba soba  8459 feb 23  2009 RNAsubopt.c
-rwxrwxrwx  1 soba soba 34427 feb 23  2009 RNAup.c

[margxenscienculo]

THANKS! I finally found the problem. I am eternal newbie. I found where is the RNAfold. It is /usr/bin. I changed and it is working.

[beauchemin.david.3]

Hello and sorry for pulling back this thread,

I have similar but not exactly the same issue since everything regarding RNAfold seems to work well but the problem rather comes from subsequent RNAduplex processing. (OS : W10). (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.

See :

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 what is going on here.

Thank you

[Pierre Lindenbaum]

ask this as a new question please.

Answer 1

[Pierre Lindenbaum]

ahem... did you compile RNAfold?

Check that option -r point to the right location. I don't known if it expects a directory or a compiled executable.

[margxenscienculo]

THANKS! I finally found the problem. I am eternal newbie. I found where is the RNAfold. It is /usr/bin. I changed and it is working.

[mickael.leclercq]

it expects a directory