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MayurDivate / GUAVA

GUAVA : A GUI tool for the Analysis and Visualization of ATAC-seq data
GNU General Public License v3.0
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An illegal reflective access operation has occurred #18

Closed swc42 closed 5 years ago

swc42 commented 5 years ago

When I run data analysis in GUAVA, I keep getting this warning and I never see the tabular output interface window. Is there anyone who can provide suggestions on how I can fix this? [awd2056a:GUAVA-1 chungs1$ java -jar GUAVA.jar GUAVA version 1 Operating System of machine :Mac OS X cutadapt: Working! bowtie: Working! bowtie2: Working! fastqc: Working! samtools: Working! macs2: Working! Picard: Working! bedtools: Working! bedGraphToBigWig: Working! igv: Working! fastq QC... Alignment... Please wait while bowtie2 alignment is finished..Done! WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.apache.poi.util.DocumentHelper (file:/Users/chungs1/GUAVA-1/lib/poi-ooxml-3.16-beta2.jar) to method com.sun.org.apache.xerces.internal.util.SecurityManager.setEntityExpansionLimit(int) WARNING: Please consider reporting this to the maintainers of org.apache.poi.util.DocumentHelper WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release ---- Alignment filtering ------ Remove duplicates...Done! Filter [chr6] reads... No chr found for idxstats
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at umac.guava.Samtools.getReadCount(Samtools.java:253) at umac.guava.AnalysisWorkflow.runAlignmentFiltering(AnalysisWorkflow.java:570) at umac.guava.AnalysisWorkflow.startGUIGuavaAnalysis(AnalysisWorkflow.java:166) at umac.guava.MainJFrame.startJButtonActionPerformed(MainJFrame.java:837) at umac.guava.MainJFrame.access$700(MainJFrame.java:27) at umac.guava.MainJFrame$8.actionPerformed(MainJFrame.java:267) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6632) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3342) at java.desktop/java.awt.Component.processEvent(Component.java:6397) at java.desktop/java.awt.Container.processEvent(Container.java:2263) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5008) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4840) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4918) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4547) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4488) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2307) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2772) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4840) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:95) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

MayurDivate commented 5 years ago

@swc42

"The illegal reflective access" is a Java 9 problem. I never faced it before. I will try my best to solve it.

But to help you with the alignment filtering problem. could you please share the log file?

Thanks, Mayur

Shirayuki-hub commented 4 years ago

Hi, I am having a similar issue here. Could you please help me?

$ java -jar GUAVA.jar GUAVA version 1 Operating System of machine :Mac OS X cutadapt: Working! bowtie: Working! bowtie2: Working! fastqc: Working! samtools: Working! macs2: Working! Picard: Working! bedtools: Working! bedGraphToBigWig: Working! igv: Working! Adapter trimming...Done fastq QC... Alignment... Please wait while bowtie2 alignment is finished..Done! WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.apache.poi.util.DocumentHelper (file:/Users/GUAVA-1/lib/poi-ooxml-3.16-beta2.jar) to method com.sun.org.apache.xerces.internal.util.SecurityManager.setEntityExpansionLimit(int) WARNING: Please consider reporting this to the maintainers of org.apache.poi.util.DocumentHelper WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release ---- Alignment filtering ------ Remove duplicates...Done! Filter [chr1] reads... Filter [chr10] reads... Filter [chr11] reads... Filter [chr11_gl000202_random] reads... Filter [chr12] reads... Filter [chr13] reads... Filter [chr14] reads... Filter [chr15] reads... Filter [chr16] reads... Filter [chr17] reads... Filter [chr17_ctg5_hap1] reads... Filter [chr17_gl000203_random] reads... Filter [chr17_gl000204_random] reads... Filter [chr17_gl000205_random] reads... Filter [chr17_gl000206_random] reads... Filter [chr18] reads... Filter [chr18_gl000207_random] reads... Filter [chr19] reads... Filter [chr19_gl000208_random] reads... Filter [chr19_gl000209_random] reads... Filter [chr1_GL456210_random] reads... Filter [chr1_GL456211_random] reads... Filter [chr1_GL456212_random] reads... Filter [chr1_GL456213_random] reads... Filter [chr1_GL456221_random] reads... Filter [chr1_gl000191_random] reads... Filter [chr1_gl000192_random] reads... Filter [chr2] reads... Filter [chr20] reads... Filter [chr21] reads... Filter [chr21_gl000210_random] reads... Filter [chr22] reads... Filter [chr3] reads... Filter [chr4] reads... Filter [chr4_GL456216_random] reads... Filter [chr4_GL456350_random] reads... Filter [chr4_JH584292_random] reads... Filter [chr4_JH584293_random] reads... Filter [chr4_JH584294_random] reads... Filter [chr4_JH584295_random] reads... Filter [chr4_ctg9_hap1] reads... Filter [chr4_gl000193_random] reads... Filter [chr4_gl000194_random] reads... Filter [chr5] reads... Filter [chr5_GL456354_random] reads... Filter [chr5_JH584296_random] reads... Filter [chr5_JH584297_random] reads... Filter [chr5_JH584298_random] reads... Filter [chr5_JH584299_random] reads... Filter [chr6_apd_hap1] reads... Filter [chr6_cox_hap2] reads... Filter [chr6_dbb_hap3] reads... Filter [chr6_mann_hap4] reads... Filter [chr6_mcf_hap5] reads... Filter [chr6_qbl_hap6] reads... Filter [chr6_ssto_hap7] reads... Filter [chr7] reads... Filter [chr7_GL456219_random] reads... Filter [chr7_gl000195_random] reads... Filter [chr8] reads... Filter [chr8_gl000196_random] reads... Filter [chr8_gl000197_random] reads... Filter [chr9] reads... Filter [chr9_gl000198_random] reads... Filter [chr9_gl000199_random] reads... Filter [chr9_gl000200_random] reads... Filter [chr9_gl000201_random] reads... Filter [chrM] reads... Filter [chrUn_GL456239] reads... Filter [chrUn_GL456359] reads... Filter [chrUn_GL456360] reads... Filter [chrUn_GL456366] reads... Filter [chrUn_GL456367] reads... Filter [chrUn_GL456368] reads... Filter [chrUn_GL456370] reads... Filter [chrUn_GL456372] reads... Filter [chrUn_GL456378] reads... Filter [chrUn_GL456379] reads... Filter [chrUn_GL456381] reads... Filter [chrUn_GL456382] reads... Filter [chrUn_GL456383] reads... Filter [chrUn_GL456385] reads... Filter [chrUn_GL456387] reads... Filter [chrUn_GL456389] reads... Filter [chrUn_GL456390] reads... Filter [chrUn_GL456392] reads... Filter [chrUn_GL456393] reads... Filter [chrUn_GL456394] reads... Filter [chrUn_GL456396] reads... Filter [chrUn_JH584304] reads... Filter [chrUn_gl000211] reads... Filter [chrUn_gl000212] reads... Filter [chrUn_gl000213] reads... Filter [chrUn_gl000214] reads... Filter [chrUn_gl000215] reads... Filter [chrUn_gl000216] reads... Filter [chrUn_gl000217] reads... Filter [chrUn_gl000218] reads... Filter [chrUn_gl000219] reads... Filter [chrUn_gl000220] reads... Filter [chrUn_gl000221] reads... Filter [chrUn_gl000222] reads... Filter [chrUn_gl000223] reads... Filter [chrUn_gl000224] reads... Filter [chrUn_gl000225] reads... Filter [chrUn_gl000226] reads... Filter [chrUn_gl000227] reads... Filter [chrUn_gl000228] reads... Filter [chrUn_gl000229] reads... Filter [chrUn_gl000230] reads... Filter [chrUn_gl000231] reads... Filter [chrUn_gl000232] reads... Filter [chrUn_gl000233] reads... Filter [chrUn_gl000234] reads... Filter [chrUn_gl000235] reads... Filter [chrUn_gl000236] reads... Filter [chrUn_gl000237] reads... Filter [chrUn_gl000238] reads... Filter [chrUn_gl000239] reads... Filter [chrUn_gl000240] reads... Filter [chrUn_gl000241] reads... Filter [chrUn_gl000242] reads... Filter [chrUn_gl000243] reads... Filter [chrUn_gl000244] reads... Filter [chrUn_gl000245] reads... Filter [chrUn_gl000246] reads... Filter [chrUn_gl000247] reads... Filter [chrUn_gl000248] reads... Filter [chrUn_gl000249] reads... Filter [chrX] reads... Filter [chrX_GL456233_random] reads... Filter [chrY] reads... Filter [chrY_JH584300_random] reads... Filter [chrY_JH584301_random] reads... Filter [chrY_JH584302_random] reads... Filter [chrY_JH584303_random] reads... No chr found for idxstats
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at umac.guava.Samtools.getReadCount(Samtools.java:253) at umac.guava.AnalysisWorkflow.runAlignmentFiltering(AnalysisWorkflow.java:570) at umac.guava.AnalysisWorkflow.startGUIGuavaAnalysis(AnalysisWorkflow.java:166) at umac.guava.MainJFrame.startJButtonActionPerformed(MainJFrame.java:837) at umac.guava.MainJFrame.access$700(MainJFrame.java:27) at umac.guava.MainJFrame$8.actionPerformed(MainJFrame.java:267) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6632) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3342) at java.desktop/java.awt.Component.processEvent(Component.java:6397) at java.desktop/java.awt.Container.processEvent(Container.java:2263) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5008) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4840) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4918) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4547) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4488) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2307) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2772) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4840) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:95) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

jademcdaniel commented 2 years ago

Hi! Thanks so much for all the work you've put into this program--it's made ATAC-seq analysis much easier for someone who is a beginner with sequencing analysis.

I've been having this same issue as listed above and I was wondering if you ever figured out a work-around. Here is what I'm seeing:

(base) drigo@drigo-Precision-5820-Tower:~$ cd ~/GUAVA-1.0.1 (base) drigo@drigo-Precision-5820-Tower:~/GUAVA-1.0.1$ java -jar GUAVA.jar GUAVA version 1 Operating System of machine :Linux cutadapt: Working! bowtie: Working! bowtie2: Working! fastqc: Working! samtools: Working! macs2: Working! Picard: Working! bedtools: Working! bedGraphToBigWig: Working! igv: Working! Adapter trimming...Done fastq QC... Alignment... Please wait while bowtie2 alignment is finished..Done! WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.apache.poi.util.DocumentHelper (file:/home/drigo/GUAVA-1.0.1/lib/poi-ooxml-3.16-beta2.jar) to method com.sun.org.apache.xerces.internal.util.SecurityManager.setEntityExpansionLimit(int) WARNING: Please consider reporting this to the maintainers of org.apache.poi.util.DocumentHelper WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release ---- Alignment filtering ------ Remove duplicates...Done! Filter [chrM] reads... No chr found for idxstats
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at umac.guava.Samtools.getReadCount(Samtools.java:253) at umac.guava.AnalysisWorkflow.runAlignmentFiltering(AnalysisWorkflow.java:570) at umac.guava.AnalysisWorkflow.startGUIGuavaAnalysis(AnalysisWorkflow.java:166) at umac.guava.MainJFrame.startJButtonActionPerformed(MainJFrame.java:837) at umac.guava.MainJFrame.access$700(MainJFrame.java:27) at umac.guava.MainJFrame$8.actionPerformed(MainJFrame.java:267) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:270) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6589) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3342) at java.desktop/java.awt.Component.processEvent(Component.java:6354) at java.desktop/java.awt.Container.processEvent(Container.java:2261) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4966) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2319) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4798) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4914) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4543) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4484) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2305) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2772) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4798) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772) at java.desktop/java.awt.EventQueue.access$600(EventQueue.java:97) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:97) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

I've attached the log file as well, but let me know if you need anything else.

7315-JM-2_S1_L005_R1_001_log.txt