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bioinfo-biols / CIRI-cookbook

Document for CIRI-series software
https://ciri-cookbook.readthedocs.io/en/latest/index.html
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CIRI-full Merge (step-by-step) #29

Closed ashleyhappiness closed 1 year ago

ashleyhappiness commented 1 year ago

I am running into an issue running the merge function. It appears to be working but then failing during the creation of the output file. Below is the log file. I'm unsure what may be going wrong and haven't had any issues with the other steps of CIRI-full. Thank you, A

classpath = bin/ Output prefix = /panfs/jay/groups/5/reedkm/shared/CIRI2/Powell_Prj015/test/sample12_merge

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, 13 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:498) 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:770) at CIRI_Full2.main(CIRI_Full2.java:551) ... 5 more

ashleyhappiness commented 1 year ago

I still haven't been able to get this to work. I can run the test data without an issue but with my own data, it keeps failing at the Merge step. My most recent run had this feedback (I am unsure what I would need to change to get it to run):

classpath = ..// Output prefix = /panfs/jay/groups/5/reedkm/shared/CIRI2/Powell_Prj015/CIRI-full/CIRI-full_v2.0/sample_1/sample1

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, 9 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:498) 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