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UcarLab / CoRE-ATAC

MIT License
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Running Feature Extraction Missing Files #1

Closed dylan6thomas closed 2 years ago

dylan6thomas commented 2 years ago

When running feature extraction according to the directions, the program returns: cat: atac_pbmc_500_v1_possorted_chr21_insertmetrics.txt: No such file or directory rm: cannot remove 'atac_pbmc_500_v1_possorted_chr21_insertmetrics.txt': No such file or directory Exception in thread "main" java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:564) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:61) Caused by: java.lang.NullPointerException at org.jax.peastools.insertmetrics.PeakInsertMetrics.getInsertMetrics(PeakInsertMetrics.java:72) at org.jax.peastools.insertmetrics.PeakInsertMetrics.main(PeakInsertMetrics.java:36) at org.jax.peastools.Main.main(Main.java:39) ... 5 more

Then when running prediction, the program returns: FileNotFoundError: [Errno 2] No such file or directory: '/data/home/dylan.thomas/CoRE-ATAC/Data/core-atac-out/peak_features/atac_pbmc_500_v1_possorted_sequencefreq.txt' It seems I am missing files that would be created with feature extraction. I am running the program in a shared server, so I did not have access to sudo rights. This meant I could not enter the sandbox directory using --writable. I'm not sure if that is what caused the problem.

ajt986 commented 2 years ago

After reviewing these error messages, the problem is occurring with this line of code:

int npi = Math.min(1,peaks.length-1); where peaks is defined as: Location[] peaks = util.getSortedLocationsWithIds(peakfile, chr);

It looks like there are no peaks available for chr21 since all this is doing is grabbing the set of peaks for a specific chromosome. I would check the peak file and see if there are peaks for chr21. If there are no peaks for chr21, I would provide a different chromosome file that only includes chromosomes that exist in the peak file.

Let me know if this solves the issue.

Best, Asa

dylan6thomas commented 2 years ago

It seems the problem was in my chromosome file, I had mistakenly forgotten to list the absolute directory. The missing files seem to be there. The extraction is running, so I will let you know when it is finished. Thank you!

Best, Dylan