User Report: Issue loading bigWig file

I contacted the user with the above information and they confirmed that they can now load bigWig files as usual.

Moving this to closed.

Paige Kulzer - Go ahead and contact the user to let them know that IGB 10.0.1 has been released, and should fix the issue they were seeing. May also be worth posting something to the Google IGB Helper Group.

The user responded that they tried the above proposed solution, but it did not work for them; IGB still stalls when they try to load a bigwig file. They are going to keep using IGB 9.1.10 in the meantime, but would like to be notified when this bug is fixed.

Hi Page,

My apologies for my late response.

I did try what you have suggested to me, regarding the simplification of the files` names, but it did not work for me. I do get the same ``Retrieving chromosomes…`` like forever.

Even changing the name of the file to just a single word, raised no results as well.

I still have the old version of IGB (9.1.10), which still works great for me, with no issues. But I would love to hear when you will fix the bug with the V10.0.0, in order to start using it.

Thank you very much for all of your input, your effort to help and your great communication as well; I highly appreciate it!

My very best wishes for a great week,

Manolis

The user sent me the contents of their IGB Log so I have added that as an attachment to this ticket.

The following warning from their Log confirms that the issue this user is experiencing is likely being caused by the presence of special characters in the folder/file names they're trying to use:

Apr 24, 2024 9:33:04 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
WARNING: The input string file:/P:/IGB files for ChIP_seqs/ChIP_seq_N8_Wt_VEL2_GFP_Verticillium dahliae/IGB/ChIP_N8_Wt_vs_VEL2_GFP/Galaxy154-[bamCoverage_Wt_N3_50_BinSize] (3).bigwig contains a URI scheme but is not a valid URI
java.lang.IllegalArgumentException: The input string file:/P:/IGB files for ChIP_seqs/ChIP_seq_N8_Wt_VEL2_GFP_Verticillium dahliae/IGB/ChIP_N8_Wt_vs_VEL2_GFP/Galaxy154-[bamCoverage_Wt_N3_50_BinSize] (3).bigwig contains a URI scheme but is not a valid URI
at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:106)
at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:78)
at com.gene.bigwighandler.BigWigSymLoader.initbbReader(BigWigSymLoader.java:89)
at com.gene.bigwighandler.BigWigSymLoader.init(BigWigSymLoader.java:62)
at com.gene.bigwighandler.BigWigSymLoader.getChromosomeList(BigWigSymLoader.java:106)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:153)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:139)
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:119)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:749)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:691)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:686)
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:305)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:342)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: java.net.URISyntaxException: Illegal character in path at index 12: file:/P:/IGB files for ChIP_seqs/ChIP_seq_N8_Wt_VEL2_GFP_Verticillium dahliae/IGB/ChIP_N8_Wt_vs_VEL2_GFP/Galaxy154-[bamCoverage_Wt_N3_50_BinSize] (3).bigwig
at java.base/java.net.URI$Parser.fail(URI.java:2995)
at java.base/java.net.URI$Parser.checkChars(URI.java:3166)
at java.base/java.net.URI$Parser.parseHierarchical(URI.java:3248)
at java.base/java.net.URI$Parser.parse(URI.java:3196)
at java.base/java.net.URI.<init>(URI.java:645)
at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:103)
... 17 more

I was able to reproduce this warning by recreating the above file path on my own computer. I was then also able to fix this issue by replacing all special characters (spaces and square brackets) with non-special characters (underscores and parentheses) before attempting to add the bigwig file to IGB. I recommended that the user do the same while we work on fixing this bug.