miRanalyzer run error

Question

[Mohammad Reza Bakhtiarizadeh]

Hi

I get into trouble when I run miRanalyzer, my command like this:

java -Xmx2000m -jar miRanalyzer.jar input=SRR069503.rc dbPath=/home/user/miRanalyzer species=dm3 speciesShort=dme kingdom=animal bowtiePath=/usr/lbin translibs=rfam:RFam:15:5

the error report as follow:
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.rangeCheck(ArrayList.java:635)
at java.util.ArrayList.get(ArrayList.java:411)
at miRanalyzerV2.IsoMiR.makeIsoMir(IsoMiR.java:105)
at miRanalyzerV2.MiRanalyzer.main(MiRanalyzer.java:142)

Can you give me some suggestion to solve this problem?
Best

[Nicola Casiraghi]

Probably is a typo, but is the bowtiePath correct? Example from miRanalyzer manual:

java -Xmx2000m -jar miRanalyzer.jar input=SRR069503.rc \
            dbPath=/home/user/miRanalyzer species=dm3 speciesShort=dme \
            kingdom=animal bowtiePath=/usr/local/bin/bowtie64 translibs=rfam:RFam:15:5

[Mohammad Reza Bakhtiarizadeh]

My bowtie path is OK. I want to run the miranalyzer test data. I checked all of paths. I really don't know what is the problem.

[Nicola Casiraghi]

I downloaded miRanalyzer and I tried to run the test data but I got your same error. Sorry, no idea to help you more.

[Mohammad Reza Bakhtiarizadeh]

Thanks so much for taking your time.

Best

Answer 1

[mozduri.z]

Jai said to me:

try with a higher spec PC. I see the error is java.lang.IndexOutOfBoundsException which comes when there is some memory issues.