Haplogroup classification issue in 1.1-beta

haansi commented 5 years ago

Used data: https://github.com/apeltzer/mitoDB-data/blob/master/data/Modern/1000GP3/1000GP3.csv https://github.com/apeltzer/mitoDB-data/blob/master/data/Modern/1000GP3/1000GP3.fasta

Clicked on Analysis -> Calculate Haplogroups

Writing fasta sequences to multifasta.fasta
Start haploGrep ....
Haplogroups are determined
java.io.FileNotFoundException: haplogroups.hsd (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at java.io.FileReader.<init>(FileReader.java:72)
    at io.reader.HSDInput.<init>(HSDInput.java:31)
    at analysis.HaplotypeCaller.update(HaplotypeCaller.java:54)
    at view.menus.AnalysisMenu.lambda$null$1(AnalysisMenu.java:84)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.concurrent.EventHelper.fireEvent(EventHelper.java:219)
    at javafx.concurrent.Task.fireEvent(Task.java:1356)
    at javafx.concurrent.Task.setState(Task.java:723)
    at javafx.concurrent.Task$TaskCallable.lambda$call$501(Task.java:1434)
    at com.sun.javafx.application.PlatformImpl.lambda$null$172(PlatformImpl.java:295)
    at java.security.AccessController.doPrivileged(Native Method)
    at com.sun.javafx.application.PlatformImpl.lambda$runLater$173(PlatformImpl.java:294)
    at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95)
    at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
    at com.sun.glass.ui.gtk.GtkApplication.lambda$null$48(GtkApplication.java:139)
    at java.lang.Thread.run(Thread.java:748)
Exception in thread "JavaFX Application Thread" java.lang.NullPointerException
    at analysis.HaplotypeCaller.update(HaplotypeCaller.java:60)
    at view.menus.AnalysisMenu.lambda$null$1(AnalysisMenu.java:84)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.concurrent.EventHelper.fireEvent(EventHelper.java:219)
    at javafx.concurrent.Task.fireEvent(Task.java:1356)
    at javafx.concurrent.Task.setState(Task.java:723)
    at javafx.concurrent.Task$TaskCallable.lambda$call$501(Task.java:1434)
    at com.sun.javafx.application.PlatformImpl.lambda$null$172(PlatformImpl.java:295)
    at java.security.AccessController.doPrivileged(Native Method)
    at com.sun.javafx.application.PlatformImpl.lambda$runLater$173(PlatformImpl.java:294)
    at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95)
    at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
    at com.sun.glass.ui.gtk.GtkApplication.lambda$null$48(GtkApplication.java:139)
    at java.lang.Thread.run(Thread.java:748)

JudithNeukamm commented 5 years ago

I tried it as well and it worked. Hm...I will at least catch this error and hope to find the problem.

haansi commented 5 years ago

FYI: have to add that I tried it on ubuntu - could it be path related issues?

JudithNeukamm commented 5 years ago

I'm running it on Ubuntu as well.

seppinho commented 5 years ago

Maybe different Java versions? @haansi can you report your java and also javafx version. Using the same input files should reproduce the bug.

haansi commented 5 years ago

java version "1.8.0_171" Java(TM) SE Runtime Environment (build 1.8.0_171-b11) Java HotSpot(TM) 64-Bit Server VM (build 25.171-b11, mixed mode)

Ubuntu 18.04.2 LTS

JudithNeukamm commented 3 years ago

Please let me know if this error still occurs in newer versions.

haansi commented 3 years ago

Hi Judith, thanks, it works! Suggestion: For large datasets it would be nice to have a progressbar, or similar to see if the process is still running

mitobench / mitoBench

Haplogroup classification issue in 1.1-beta #70