Epinano_variant.py terminated with no error message

[BioinfoHub-PeiQinNg]

Hi there. I am trying to run EpiNano1.2 on some RNA direct data. When I check the log files of the submitted job for EpiNano_variant.py, it showed the following log with no error message.

Process Process-2: Traceback (most recent call last): File "/home/ng/localenv/miniconda3/envs/Epinano1.2/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/ng/localenv/miniconda3/envs/Epinano1.2/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/ng/localenv/EpiNano/Epinano_Variants.py", line 44, in split_tsv_for_per_site_var_freq head = next(tsv) StopIteration

The code that I used to run EpiNano1.2 is as follow: python ~/localenv/EpiNano/Epinano_Variants.py \ -R {input.ref} \ -b {input.bam} \ -s /home/ng/localenv/EpiNano/misc/sam2tsv.jar \ -T g Thank you. If you can help me with this that will be great!

[BioinfoHub-PeiQinNg]

A little bit more information on the issue:

I have looked at the previous thread #94 and tried the following command line:

samtools view -h -F 3860 {bam_file} | java -jar {sam2tsv} -r {reference_file}

And this is the output I get:

xception in thread "main" java.lang.UnsupportedClassVersionError: com/github/lindenb/jvarkit/tools/sam2tsv/Sam2Tsv : Unsupported major.minor version 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:808) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:443) at java.net.URLClassLoader.access$100(URLClassLoader.java:65) at java.net.URLClassLoader$1.run(URLClassLoader.java:355) at java.net.URLClassLoader$1.run(URLClassLoader.java:349) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:348) at java.lang.ClassLoader.loadClass(ClassLoader.java:430) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:326) at java.lang.ClassLoader.loadClass(ClassLoader.java:363) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482) I am not quite sure if this is the reason to the StopIteration issue. Will be looking forward to hear back from you on this. Thank you!

[Huanle]

Hi @BioinfoHub-PeiQinNg , Thanks for using epinano. May I know which version of sam2tsv.jar you are using? You are expected to use the one included in the Epinano git repository. Hope this helps.

[BioinfoHub-PeiQinNg]

Hi Huan.

Thank you for replying. I have reinstalled the repo using git clone https://github.com/novoalab/EpiNano and reran the samtools command just to be sure I am using the current sam2tsv.jar.

It still gives the same error message. Any ideas how I can resolve this?

[Huanle]

Have you run samtools view -h -F 3860 {bam_file} | java -jar {sam2tsv} -r {reference_file} and see any outputs?

[BioinfoHub-PeiQinNg]

Hi Huan,

Yes I did. Still the same error message as the one I have posted.

I have attached the error message for reference samtools view -h -F 3860 H10_Heads_R1_RNAD.bam | java -jar /home/ng/localenv/EpiNano/misc/sam2tsv.jar -r /data/processing1/sabrina_ng/ref/genome.fasta Exception in thread "main" java.lang.UnsupportedClassVersionError: com/github/lindenb/jvarkit/tools/sam2tsv/Sam2Tsv : Unsupported major.minor version 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:808) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:443) at java.net.URLClassLoader.access$100(URLClassLoader.java:65) at java.net.URLClassLoader$1.run(URLClassLoader.java:355) at java.net.URLClassLoader$1.run(URLClassLoader.java:349) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:348) at java.lang.ClassLoader.loadClass(ClassLoader.java:430) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:326) at java.lang.ClassLoader.loadClass(ClassLoader.java:363) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

[Huanle]

Hi @BioinfoHub-PeiQinNg ,

this seems to be an error associated with Java version. I recommend updating your java and try again.

[BioinfoHub-PeiQinNg]

Yep! That fixes it! Thank you