mirDup. MicroRNA prediction. java Error software [solved]
1
0
Entering edit mode
8.0 years ago

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
Tool java mirDup MicroRNA • 2.7k views
ADD COMMENT
0
Entering edit mode

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/

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
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
ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

ask this as a new question please.

ADD REPLY
4
Entering edit mode
8.0 years ago

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.

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

it expects a directory

ADD REPLY

Login before adding your answer.

Traffic: 941 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6