Comments (3)
You did everything right. The error occurred due to you system configurations, not MiXCR. You did the right thing to fix it with unset DISPLAY
. MiXCR uses this systems dependencies for plots generation.
from mixcr.
Hi,
It seems like a known bug that we have already fixed in the develop version. Can you please try and let me know if it helped.
from mixcr.
Hi,
Thanks so much for your prompt reply! When using the develop version, I initially got the following error:
App version: 4.6.0-50-develop; built=Tue Jan 30 05:44:49 PST 2024; rev=b5ebb71cb7; lib=repseqio.v4.0
java.awt.AWTError: Can't connect to X11 window server using 'localhost:46.0' as the value of the DISPLAY variable.
at java.desktop/sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
at java.desktop/sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:102)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment.java:61)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:315)
at java.desktop/java.awt.GraphicsEnvironment$LocalGE.createGE(GraphicsEnvironment.java:101)
at java.desktop/java.awt.GraphicsEnvironment$LocalGE.<clinit>(GraphicsEnvironment.java:83)
at java.desktop/java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:129)
at java.desktop/java.awt.image.BufferedImage.createGraphics(BufferedImage.java:1181)
at org.apache.fop.svg.PDFGraphics2D.<init>(PDFGraphics2D.java:1724)
at org.apache.fop.svg.PDFDocumentGraphics2D.<init>(PDFDocumentGraphics2D.java:100)
at org.apache.fop.svg.PDFTranscoder.transcode(PDFTranscoder.java:112)
at org.apache.batik.transcoder.XMLAbstractTranscoder.transcode(XMLAbstractTranscoder.java:142)
at org.apache.batik.transcoder.SVGAbstractTranscoder.transcode(SVGAbstractTranscoder.java:158)
at com.milaboratory.miplots.ExportKt.toBytes(Export.kt:165)
at com.milaboratory.miplots.ExportKt.toPDF(Export.kt:56)
at com.milaboratory.miplots.ExportKt.toPDF(Export.kt:54)
at com.milaboratory.miplots.ExportKt.writePDFFigure(Export.kt:198)
at com.milaboratory.mixcr.cli.CommandExportShmTreesPlots.run1(SourceFile:163)
at com.milaboratory.mixcr.cli.MiXCRCommandWithOutputs.run0(SourceFile:69)
at com.milaboratory.mixcr.cli.MiXCRCommand.run(SourceFile:37)
at picocli.CommandLine.executeUserObject(CommandLine.java:1939)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)
at com.milaboratory.mixcr.cli.Main.registerLogger$lambda-27(SourceFile:514)
at picocli.CommandLine.execute(CommandLine.java:2078)
at com.milaboratory.mixcr.cli.Main.main(SourceFile:101)
At the beginning of my bash run script, I added the following line:
unset DISPLAY
And, it now seems to be working! I've got trees! Let me know if you have an alternative solution though :)
Thanks again!
from mixcr.
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