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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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Summary | Fix error | Fix bug preventing bigwig/bigbed files from loading |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Summary | Fix bug preventing bigwig/bigbed files from loading | User Report: Issue loading bigWig file |
| 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:
{quote}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, Manolis FYI: By the way the 9.1.10 version has just worked great, with the same files the new version 10.0.0 failed.{quote} Task: Fix the error causing bigwig and bigbed files to load in IGB 10.0.0. Then, release a new version of IGB with these changes ASAP and post an update to the Google Group. |
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:
{quote}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, Manolis FYI: By the way the 9.1.10 version has just worked great, with the same files the new version 10.0.0 failed.{quote} |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Sprint | Spring 8 [ 192 ] | Spring 9 [ 193 ] |
| Attachment | UserReport_Manolis_IGBLog.txt [ 18346 ] |
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
| Assignee | Paige Kulzer [ pkulzer ] |
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.
I contacted the user with the above information and they confirmed that they can now load bigWig files as usual.
Moving this to closed.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
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.