<p>I have an issue running a module trying to detect circRNA from RNAseq data. The error is a java error and I have not knowledge of java so I don't understand the issues and googling hasn't helped.
the issue arises when I try to run this module of the algorithm
<a href="https://ciri-cookbook.readthedocs.io/en/latest/CIRI-full.html#the-merge-module" rel="nofollow noreferrer">https://ciri-cookbook.readthedocs.io/en/latest/CIRI-full.html#the-merge-module</a>
as I try to run the module I get the following output and error</p>
<pre><code>Merge module start

Loading Annotation...
Annotation Loaded
Loading CIRI_AS output...
CIRI_AS output Loaded
Loading CIRI output...
CIRI output Loaded
Loading CIRI_RO output...
CIRI_RO output Loaded
Combine AS and RO output
Combine completed, 71 reads are used
Exception in thread &quot;main&quot; java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:483)
        at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.NullPointerException
        at Exon_gtf.get_exon(Exon_gtf.java:16)
        at Merge3.getmerge(Merge3.java:784)
        at CIRI_Full2.main(CIRI_Full2.java:551)
        ... 5 more
</code></pre>
<p>All prior steps preceding this one seem to have run properly and I was able to generate all the files to run the Merge module.
any help or explanation as to what the issue could be would be greatly appreciated. As I mentioned before I have no experience in java.
kind regards</p>

CC BY-SA 4.0
2021-09-09T17:55:11.600Z
Whatever the reason, it shouldn't crash with a null pointer exception.  You should bring that to the attention of the developers so they can try to debug.  Does it run successfully with their [test dataset](https://ciri-cookbook.readthedocs.io/en/latest/CIRI-full.html#how-to-run-the-test-data-set-using-ciri-full)?  That might help narrow it down.
Jesse
CC BY-SA 4.0
2021-09-10T06:51:33.520Z
Hi Jesse, I did bring it up on github but no response so far. I have run the same pipeline of another dataset of mine and it worked. So the issue might be data I am feeding it. Thanks
Elhadi Iich
CC BY-SA 4.0
2021-09-10T15:33:46.860Z
Makes sense (something about the input data crashing the software).  It might be meaningful that the crash is within a GTF-handling function, too.  Are you giving it the optional GTF annotation file, and if so, does that same file work with the other dataset?  If you can make a small enough reproducible test case to post here that shows the crash, maybe someone can help narrow it down.
Jesse
CC BY-SA 4.0
2021-09-12T00:46:17.877Z
thanks for the feedback. I don't use the optional GTF. Comparing the inputs for that piece of code there is a clear difference in size so that means the difference is in there. I discussed with our collaborator who generated the data and they did process it differently compared to the previous one that did work. So the problem is not the code but the input and how the data was generated.
Elhadi Iich
<rna-seq><java>
java error when running CIRI-full.jar Merge module
# java error when running CIRI-full.jar Merge module

(Asked by: username_0 on 2021-09-02)

I have an issue running a module trying to detect circRNA from RNAseq data. The error is a java error and I have not knowledge of java so I don't understand the issues and googling hasn't helped.
the issue arises when I try to run this module of the algorithm
https://ciri-cookbook.readthedocs.io/en/latest/CIRI-full.html#the-merge-module
as I try to run the module I get the following output and error
Merge module start

Loading Annotation...
Annotation Loaded
Loading CIRI_AS output...
CIRI_AS output Loaded
Loading CIRI output...
CIRI output Loaded
Loading CIRI_RO output...
CIRI_RO output Loaded
Combine AS and RO output
Combine completed, 71 reads are used
Exception in thread "main" java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:483)
        at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.NullPointerException
        at Exon_gtf.get_exon(Exon_gtf.java:16)
        at Merge3.getmerge(Merge3.java:784)
        at CIRI_Full2.main(CIRI_Full2.java:551)
        ... 5 more

All prior steps preceding this one seem to have run properly and I was able to generate all the files to run the Merge module.
any help or explanation as to what the issue could be would be greatly appreciated. As I mentioned before I have no experience in java.
kind regards

**Tags:** rna-seq, java
> **Comments:**
> **username_1**: Whatever the reason, it shouldn't crash with a null pointer exception.  You should bring that to the attention of the developers so they can try to debug.  Does it run successfully with their [test dataset](https://ciri-cookbook.readthedocs.io/en/latest/CIRI-full.html#how-to-run-the-test-data-set-using-ciri-full)?  That might help narrow it down.  
> **username_0**: Hi Jesse, I did bring it up on github but no response so far. I have run the same pipeline of another dataset of mine and it worked. So the issue might be data I am feeding it. Thanks  
> **username_1**: Makes sense (something about the input data crashing the software).  It might be meaningful that the crash is within a GTF-handling function, too.  Are you giving it the optional GTF annotation file, and if so, does that same file work with the other dataset?  If you can make a small enough reproducible test case to post here that shows the crash, maybe someone can help narrow it down.  
> **username_0**: thanks for the feedback. I don't use the optional GTF. Comparing the inputs for that piece of code there is a clear difference in size so that means the difference is in there. I discussed with our collaborator who generated the data and they did process it differently compared to the previous one that did work. So the problem is not the code but the input and how the data was generated.  

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## 0 answers

