Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Critical
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 9
Description
Situation: Several IGB users have reached out describing an issue occurring when they try to load bigwig and bigbed files in IGB 10.0.0. It appears that this is caused by the occurrence of special characters, such as spaces, in the file's name or a folder name that the file is within. Here's the latest email from a user describing this issue:
Dear IGB Team,
Yesterday, I updated the IGB in my desktop to the latest version 10.0.0.
Since then my IGB does not work properly any more. No matter which genome I'm going to use (Arabidopsis thaliana, Aspergillus nidulans or others), it seems, initially, that the genome file with the corresponding .gff3s files are loaded, but when I`m trying to upload my ChIP-seq .bigwig files as well (which I have used successfully plenty of times in the past with the previous version of IGB), it appears at the bottom left of the screen that there are is a short of retrieving information about chromosomes but it actually the whole process never ends with a final result to not be able to visualize my ChIP-seq data with from diff. organisms that it was a matter of minutes to do with the older version of IGB.
Could you please help me with that issue?
Best wishes,
ManolisFYI: By the way the 9.1.10 version has just worked great, with the same files the new version 10.0.0 failed.
Attachments
Issue Links
- relates to
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IGBF-3670 Fix IGB unable to load files/folders with spaces
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- Closed
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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:
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.