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UcarLab / PEAS

Code repository for PEAS (Predict Enhancers from ATAC-seq), including feature extraction files and easy to use python script for training enhancer models and predicting enhancers using MLP Neural Networks.
MIT License
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thresh.txt #6

Open ph09 opened 2 years ago

ph09 commented 2 years ago

cat: thresh.txt: No such file or directory

Is this a file that I would need to provide? Or it is an issue with PEASTools.jar?

--- Getting insert size threshold. --- 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:497) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:61) Caused by: java.lang.NullPointerException at java.util.TreeMap.put(TreeMap.java:563) at org.jax.peastools.insertmetrics.PeakThreshold.getThreshold(PeakThreshold.java:85) at org.jax.peastools.insertmetrics.PeakThreshold.doIt(PeakThreshold.java:62) at org.jax.peastools.insertmetrics.PeakThreshold.main(PeakThreshold.java:36) at org.jax.peastools.Main.main(Main.java:34) ... 5 more cat: thresh.txt: No such file or directory

ajt986 commented 2 years ago

PEASTools.jar is supposed to write the thresh.txt file. For some reason the data structure storing the chromosome writers is throwing a null pointer exception upon initialization. My best guess is that it's not reading the input chromosomes correctly. Are you providing your own chromosomes? It's also possible that the last arguments to the shell script are being incorrectly loaded as a chromosome file.