Situation: I am seeing the below error when loading data via BioViz Connect. To reproduce the issue, follow the instructions here.
Task: Investigate the issue to determine the cause. If a fix is possible, modify this ticket and fix the issue.
htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: /Users/lorainelab/.igb/fileCache/ZGF0YS5jeXZlcnNlLm9yZy9kYXYtYW5vbi9pcGxhbnQvaG9tZS9zaGFyZWQvQmlvVml6L3JuYXNlcS9BX3RoYWxpYW5hX0p1bl8y/MDA5L1NSUDIyMDE1Ny9yZWFkcy9TUlIxMDA2MDkwNS5iYW0uYmFp/cache/data.dat (No such file or directory)
at htsjdk.samtools.FileInputResource$1.get(SamInputResource.java:247)
at htsjdk.samtools.FileInputResource$1.get(SamInputResource.java:241)
at htsjdk.samtools.util.Lazy.get(Lazy.java:25)
at htsjdk.samtools.FileInputResource.asUnbufferedSeekableStream(SamInputResource.java:282)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:341)
at org.lorainelab.igb.bam.BAM.getSAMFileReader(BAM.java:114)
at org.lorainelab.igb.bam.BAM.init(BAM.java:158)
at org.lorainelab.igb.bam.XAM.getChromosomeList(XAM.java:100)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1005)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:995)
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)
Caused by: java.io.FileNotFoundException: /Users/lorainelab/.igb/fileCache/ZGF0YS5jeXZlcnNlLm9yZy9kYXYtYW5vbi9pcGxhbnQvaG9tZS9zaGFyZWQvQmlvVml6L3JuYXNlcS9BX3RoYWxpYW5hX0p1bl8y/MDA5L1NSUDIyMDE1Ny9yZWFkcy9TUlIxMDA2MDkwNS5iYW0uYmFp/cache/data.dat (No such file or directory)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
at htsjdk.samtools.seekablestream.SeekableFileStream.<init>(SeekableFileStream.java:47)
at htsjdk.samtools.FileInputResource$1.get(SamInputResource.java:245)
... 16 more
Bug
Major
IGBF-3379 Edit SCR annotations to use R6 instead of R5 syntax and observe the effects