Exception in thread "Image Fetcher 0" java.lang.UnsatisfiedLinkError

[jstaszki]

Hi! GUAVA installation went fine! configure.sh seemed to do its job! Guava (ATAC-seq Data Analysis) starts, works, and then...

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! ---- Alignment filtering ------ Remove duplicates...Done! Filter [] reads... Done! filter blacklist...Done! Alignment shifting...Done! Generating Data tracks...Done! Fragmentsize size distribution...Done! Peak calling...Done! Fragmentsize plot...Done ! Exception in thread "AWT-EventQueue-0" java.lang.UnsatisfiedLinkError: com.sun.imageio.plugins.jpeg.JPEGImageReader.initReaderIDs(Ljava/lang/Class;Ljava/lang/Class;Ljava/lang/Class;)V at com.sun.imageio.plugins.jpeg.JPEGImageReader.initReaderIDs(Native Method) at com.sun.imageio.plugins.jpeg.JPEGImageReader.(JPEGImageReader.java:96) at com.sun.imageio.plugins.jpeg.JPEGImageReaderSpi.createReaderInstance(JPEGImageReaderSpi.java:85) at javax.imageio.spi.ImageReaderSpi.createReaderInstance(ImageReaderSpi.java:320) at javax.imageio.ImageIO$ImageReaderIterator.next(ImageIO.java:529) at javax.imageio.ImageIO$ImageReaderIterator.next(ImageIO.java:513) at org.apache.poi.ss.util.ImageUtils.getImageDimension(ImageUtils.java:76) at org.apache.poi.ss.util.ImageUtils.setPreferredSize(ImageUtils.java:146) at org.apache.poi.xssf.usermodel.XSSFPicture.getPreferredSize(XSSFPicture.java:221) at org.apache.poi.xssf.usermodel.XSSFPicture.resize(XSSFPicture.java:180) at umac.guava.ExcelPrinter.printImage(ExcelPrinter.java:853) at umac.guava.ExcelPrinter.printImage(ExcelPrinter.java:830) at umac.guava.AnalysisWorkflow.startGUIGuavaAnalysis(AnalysisWorkflow.java:208) at umac.guava.MainJFrame.startJButtonActionPerformed(MainJFrame.java:837) at umac.guava.MainJFrame.access$700(MainJFrame.java:27) at umac.guava.MainJFrame$8.actionPerformed(MainJFrame.java:267) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252) at java.awt.Component.processMouseEvent(Component.java:6525) at javax.swing.JComponent.processMouseEvent(JComponent.java:3321) at java.awt.Component.processEvent(Component.java:6290) at java.awt.Container.processEvent(Container.java:2234) at java.awt.Component.dispatchEventImpl(Component.java:4881) at java.awt.Container.dispatchEventImpl(Container.java:2292) at java.awt.Component.dispatchEvent(Component.java:4703) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) at java.awt.Container.dispatchEventImpl(Container.java:2278) at java.awt.Window.dispatchEventImpl(Window.java:2739) at java.awt.Component.dispatchEvent(Component.java:4703) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:746) at java.awt.EventQueue.access$400(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:697) at java.awt.EventQueue$3.run(EventQueue.java:691) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:719) at java.awt.EventQueue$4.run(EventQueue.java:717) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) at java.awt.EventQueue.dispatchEvent(EventQueue.java:716) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Pretty similar after 'Differential Analysis'.....

R2D2:GUAVA-1 r2d2$ java -jar GUAVA.jar GUAVA version 1 bedtools: Working! bedGraphToBigWig: Working! igv: Working! samtools: Working! /Applications/GUAVA-1/SampleData/Output/Results/Demo_GUAVA_Differental_analysis ---------- Create read count matrix ---------- BYL719_Rep1_R1_peaks.narrowPeak == 96090 BYL719_Rep2_R1_peaks.narrowPeak == 57281 DMSO_Rep1_R1_peaks.narrowPeak == 90681 DMSO_Rep2_R1_peaks.narrowPeak == 130587 ---------- Run DESeq2 code ---------- ---------- Display volcano plot ---------- Exception in thread "Image Fetcher 0" java.lang.UnsatisfiedLinkError: sun.awt.image.JPEGImageDecoder.initIDs(Ljava/lang/Class;)V at sun.awt.image.JPEGImageDecoder.initIDs(Native Method) at sun.awt.image.JPEGImageDecoder.(JPEGImageDecoder.java:63) at sun.awt.image.InputStreamImageSource.getDecoder(InputStreamImageSource.java:237) at sun.awt.image.FileImageSource.getDecoder(FileImageSource.java:77) at sun.awt.image.InputStreamImageSource.doFetch(InputStreamImageSource.java:263) at sun.awt.image.ImageFetcher.fetchloop(ImageFetcher.java:205) at sun.awt.image.ImageFetcher.run(ImageFetcher.java:169)

I'll appreciate any help with that!

[MayurDivate]

Hi,

It looks like a Java version issue. Please update the Java and give a try. Which Java version are you using?

Best wishes! Mayur

[jstaszki]

Hi!

Thanks for prompt respond. Here's what I get after 'java -version' command:

java version "1.8.0_25"

Java(TM) SE Runtime Environment (build 1.8.0_25-b17)

Java HotSpot(TM) 64-Bit Server VM (build 25.25-b02, mixed mode)

Jarek

On Wed, Aug 29, 2018 at 10:46 PM Mayur Divate notifications@github.com wrote:

Hi,

It looks like a Java version issue. Please update the Java and give a try. Which Java version are you using?

Best wishes! Mayur

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MayurDivate/GUAVASourceCode/issues/1#issuecomment-417180700, or mute the thread https://github.com/notifications/unsubscribe-auth/Ao1Xe2rSZacduGcS3aDcsZeJnufaF4B8ks5uV2AHgaJpZM4WSL1s .

-- Jarek

[MayurDivate]

Hi Jarek,

Have you tried re-installing Java?

Mayur

[jstaszki]

Mayur,

Sorry for delay. As you recommended I re-installed java. GUAVA works! But with your sample files all is fine. I can process/prepare my files, but differential analysis stops; I guess at DESeq. Here's a log file. I hope you can tell what's wrong.

Best,

Jarek

On Fri, Aug 31, 2018 at 4:09 AM Mayur Divate notifications@github.com wrote:

Hi Jarek,

Have you tried re-installing Java?

Mayur

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MayurDivate/GUAVASourceCode/issues/1#issuecomment-417603309, or mute the thread https://github.com/notifications/unsubscribe-auth/Ao1XeyIOaPJmVfCN4ca1LhtjuMlIQTEfks5uWP0ugaJpZM4WSL1s .

-- Jarek

#######################################################

Project summary

Name of the project: MyMEFsTest

Genome build: mm9

Pvalue: 0.05

Foldchange: 2.0

Upstream: 5000

Downstream: 3000

Input files

Treatment REP I bam: DFFHA_S13-R1_aligned_ATACseq.bam

Treatment REP I narrowPeak: DFFHA_S13-R1_peaks.narrowPeak

Treatment REP II bam: DFFHB_S7-R1_aligned_ATACseq.bam

Treatment REP II narrowPeak: DFFHB_S7-R1_peaks.narrowPeak

Control REP I bam: NFDHA_S9-R1_aligned_ATACseq.bam

Control REP I narrowPeak: NFDHA_S9-R1_peaks.narrowPeak

Control REP II bam: NFDHB_S22-R1_aligned_ATACseq.bam

Control REP II narrowPeak: NFDHB_S22-R1_peaks.narrowPeak

#######################################################

--------- DESeq2 --------- -------1-----------------------

    ==========     _____ _    _ ____  _____  ______          _____  
    =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
      =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
        ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
          ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
    ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
   Rsubread 1.28.1

//========================== featureCounts setting ===========================\						Input files : 4 BAM files				P /Users/r2d2/Documents/Jarek/ATACprojects/M ...				P /Users/r2d2/Documents/Jarek/ATACprojects/M ...				P /Users/r2d2/Documents/Jarek/ATACprojects/M ...				P /Users/r2d2/Document /Jarek/ATACprojects/M ...
Dir for temp files : .
Threads : 12
Level : meta-feature level
Paired-end : yes
Strand specific : no
Multimapping reads : counted
Multi-overlapping reads : not counted
Min overlapping bases : 1
Chimeric reads : not counted
Both ends mapped : required

\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\						Load annotation file ./.Rsubread_UserProvidedAnnotation_pid1272 ...				Features : 432				Meta-features : 432				Chromosomes/contigs : 23
Process BAM file /Users/r2d2/Documents/Jarek/ATACprojects/MEFs/Guava/D ...
Paired-end reads are included.
Assign fragments (read pairs) to features...
WARNING: reads from the same pair were found not adjacent to each
other in the input (due to read sorting by location or
reporting of multi-mapping read pairs).
Read re-ordering is performed.
Total fragments : 2689603
Successfully assigned fragments : 3156 (0.1%)
Running time : 0.02 minutes
Process BAM file /Users/r2d2/Documents/Jarek/ATACprojects/MEFs/Guava/D ...
Paired-end reads are included.
Assign fragments (read pairs) to features...
WARNING: reads from the same pair were found not adjacent to each
other in the input (due to read sorting by location or
reporting of multi-mapping read pairs).
Read re-ordering is performed.
Total fragments : 4600265
Successfully assigned fragments : 3563 (0.1%)
Running time : 0.03 minutes
Process BAM file /Users/r2d2/Documents/Jarek/ATACprojects/MEFs/Guava/N ...
Paired-end reads are included.
Assign fragments (read pairs) to features...
WARNING: reads from the same pair were found not adjacent to each
other in the input (due to read sorting by location or
reporting of multi-mapping read pairs).
Read re-ordering is performed.
Total fragments : 5648849
Successfully assigned fragments : 9813 (0.2%)
Running time : 0.04 minutes
Process BAM file /Users/r2d2/Documents/Jarek/ATACprojects/MEFs/Guava/N ...
Paired-end reads are included.
Assign fragments (read pairs) to features...
WARNING: reads from the same pair were found not adjacent to each
other in the input (due to read sorting by location or
reporting of multi-mapping read pairs).
Read re-ordering is performed.
Total fragments : 5009104
Successfully assigned fragments : 9179 (0.2%)
Running time : 0.03 minutes
Read assignment finished.

\===================== http://subread.sourceforge.net/ ======================//

---

2____ Loading required package: S4Vectors Loading required package: methods Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

expand.grid

Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

anyMissing, rowMedians

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from ‘package:base’:

apply

estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing Error in vst(dds, blind = FALSE) : less than 'nsub' rows, it is recommended to use varianceStabilizingTransformation directly Execution halted

---

[MayurDivate]

Hi Jarek,

This is the first time I am seeing this error in guava. I will have to check what's wrong. Right now, I am traveling and shifting to a different place.

Would you mind if I reply once I am free?

best wishes! Mayur

[jstaszki]

No rushing, take your time. Thanks, Jarek

On Sat, Sep 8, 2018 at 10:31 PM Mayur Divate notifications@github.com wrote:

Hi Jarek,

This is the first time I am seeing this error in guava. I will have to check what's wrong. Right now, I am traveling and shifting to a different place.

Would you mind if I reply once I am free?

best wishes!

Mayur

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MayurDivate/GUAVASourceCode/issues/1#issuecomment-419688236, or mute the thread https://github.com/notifications/unsubscribe-auth/Ao1Xew7idHzDd1KKGgQ1jnjJ-fmdsvDaks5uZIuFgaJpZM4WSL1s .

-- Jarek

[MayurDivate]

Hi Jarek,

By any chance, have you figured it out? I tried a fresh installation on my new machine, it is working for me.

Thanks, Mayur

[jstaszki]

Hi Mayur,

I gave up; maybe one day I’ll try again.

Thanks,

Jarek

On Nov 27, 2018, at 5:56 PM, Mayur Divate notifications@github.com wrote:

Hi Jarek,

By any chance, have you figured it out? I tried a fresh installation on my new machine, it is working for me.

Thanks, Mayur

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MayurDivate/GUAVASourceCode/issues/1#issuecomment-442264437, or mute the thread https://github.com/notifications/unsubscribe-auth/Ao1Xe9TpxCgETLagccTiGZijyK1_PbCtks5uzdEvgaJpZM4WSL1s.