Entering edit mode
8.9 years ago
margxenscienculo ▴ 50
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
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/
I had downloaded it. v 1.8.5 and v 2.1.7. Nothing version works.
show us the ouput of `ls -la
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.
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.
So I'm wondering what is going on here.
ask this as a new question please.