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Troubles launch IGV on windows #1512

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projassanchez opened this issue Apr 17, 2024 · 12 comments
Open

Troubles launch IGV on windows #1512

projassanchez opened this issue Apr 17, 2024 · 12 comments
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@jrobinso
Milestone
2.19.0

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@projassanchez
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Hello, I am having issues by launching IGV on windows. It seems to be loading resources but it remains at this stage forever:

WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
java version "17.0.10" 2024-01-16 LTS
Java(TM) SE Runtime Environment (build 17.0.10+11-LTS-240)
Java HotSpot(TM) 64-Bit Server VM (build 17.0.10+11-LTS-240, mixed mode, sharing)
INFO [Apr 17,2024 15:47] [Main] Startup  IGV Version 2.17.4 03/26/2024 12:38 PM
INFO [Apr 17,2024 15:47] [Main] Java 17.0.10 (build 17.0.10+11-LTS-240) 2024-01-16
INFO [Apr 17,2024 15:47] [Main] Java Vendor: Oracle Corporation https://java.oracle.com/
INFO [Apr 17,2024 15:47] [Main] JVM: Java HotSpot(TM) 64-Bit Server VM
INFO [Apr 17,2024 15:47] [Main] OS: Windows 11 10.0 amd64
INFO [Apr 17,2024 15:47] [Main] IGV Directory: C:\Users\PatriciaRojas-Sanche\igv
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO [Apr 17,2024 15:47] [AmazonUtils] AWS default credentials found. AWS support enabled.
INFO [Apr 17,2024 15:47] [CommandListener] Listening on port 60151
INFO [Apr 17,2024 15:47] [GenomeManager] Loading genome: C:\...\igv\genomes\hg38.json
INFO [Apr 17,2024 15:47] [TrackLoader] Loading resource:  https://hgdownload.soe.ucsc.edu/gbdb/hg38/mane/mane.bb
INFO [Apr 17,2024 15:47] [TrackLoader] Loading resource:  https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz
@jrobinso
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I'm not able to reproduce the issue. What exactly do you see? Is the wait cursor showing? We encountered a bug in another situation in which the wait cursor was not dismissed, giving the appearance that IGV was frozen. However it was just the cursor, doing anything (for example selecting a chromosome) worked as normal and the cursor would then dismiss.

A second observation, but this should not matter, we do not have nor test IGV with Oracle Java. You might try the IGV download with "Java included".

@projassanchez
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Thank you for your fast reply. I see nothing else (the browser doesn't open) just the terminal
I've tried to install it with java included but the issue seems to be the same (but in this case the terminal and the browser don't open)

@palsilva
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Hello, I am having issues by launching IGV on windows. It seems to be loading resources but it remains at this stage forever:

WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
java version "17.0.10" 2024-01-16 LTS
Java(TM) SE Runtime Environment (build 17.0.10+11-LTS-240)
Java HotSpot(TM) 64-Bit Server VM (build 17.0.10+11-LTS-240, mixed mode, sharing)
INFO [Apr 17,2024 15:47] [Main] Startup  IGV Version 2.17.4 03/26/2024 12:38 PM
INFO [Apr 17,2024 15:47] [Main] Java 17.0.10 (build 17.0.10+11-LTS-240) 2024-01-16
INFO [Apr 17,2024 15:47] [Main] Java Vendor: Oracle Corporation https://java.oracle.com/
INFO [Apr 17,2024 15:47] [Main] JVM: Java HotSpot(TM) 64-Bit Server VM
INFO [Apr 17,2024 15:47] [Main] OS: Windows 11 10.0 amd64
INFO [Apr 17,2024 15:47] [Main] IGV Directory: C:\Users\PatriciaRojas-Sanche\igv
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO [Apr 17,2024 15:47] [AmazonUtils] AWS default credentials found. AWS support enabled.
INFO [Apr 17,2024 15:47] [CommandListener] Listening on port 60151
INFO [Apr 17,2024 15:47] [GenomeManager] Loading genome: C:\...\igv\genomes\hg38.json
INFO [Apr 17,2024 15:47] [TrackLoader] Loading resource:  https://hgdownload.soe.ucsc.edu/gbdb/hg38/mane/mane.bb
INFO [Apr 17,2024 15:47] [TrackLoader] Loading resource:  https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz

I've been having the same problem since yesterday... My colleagues as well. The IGV app also doesn't seem to be working...

@jrobinso
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We can't reproduce the problem here. If you have more details please post them.

@jrobinso
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One suggestion, see if you are able to download the following from a web browser

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz

@projassanchez
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I can download it indeed. Should I put it in a specific path?

@jrobinso
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@projassanchez No this was just a test of your ability to reach it. I don't have a theory why you can't launch IGV at the moment. Were you able to launch it in the past, and did anything else change on your local computer?

Another test we can do is try to launch an earlier version. Below is a link to an installer for 2.16.2. This is not a solution but will give us some information.

@kunmonster
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Hi, I have got the same problem as this issue, and i have tried to reinstall the jdk or reinstall some other version igvs but it still didn't work. Later, I found a solution for this problem for igv-2.16.* and igv-2.18, i didn't try other version. You can try with my method.

  • find the igv config directory and open that dir (the location of mine is C:/Users/your_user_name/igv)
  • delete the file named as prefs.properties
  • re-open the igv, you can find the problem resolved

@Alan-Collins
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The above steps worked for me. Looking a bit closer at the contents of that file before and after the change I found that the "IGV.Bounds" value is causing the issue in my case. Adding the following to my prefs.properties file is sufficient to cause the issue on my system:

IGV.Bounds=30,-926,1150,800

After adding that I get the following error:

WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
WARNING: Unknown module: jide.common specified to --add-exports
java version "17.0.11" 2024-04-16 LTS
Java(TM) SE Runtime Environment (build 17.0.11+7-LTS-207)
Java HotSpot(TM) 64-Bit Server VM (build 17.0.11+7-LTS-207, mixed mode, sharing)
INFO [Sep 22,2024 20:34] [Main] Startup  IGV Version 2.18.2 08/21/2024 12:06 PM
INFO [Sep 22,2024 20:34] [Main] Java 17.0.11 (build 17.0.11+7-LTS-207) 2024-04-16
INFO [Sep 22,2024 20:34] [Main] Java Vendor: Oracle Corporation https://java.oracle.com/
INFO [Sep 22,2024 20:34] [Main] JVM: Java HotSpot(TM) 64-Bit Server VM
INFO [Sep 22,2024 20:34] [Main] OS: Windows 10 10.0 amd64
INFO [Sep 22,2024 20:34] [Main] IGV Directory: C:\Users\alanc\igv
INFO [Sep 22,2024 20:34] [CommandListener] Listening on port 60151
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO [Sep 22,2024 20:34] [GenomeManager] Loading genome: https://igv.org/genomes/json/hg38.json
INFO [Sep 22,2024 20:34] [TrackLoader] Loading resource:  https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz

My prefs.properties file had previously also specified the following, but IGV still launched fine with those in the file.

SHOW_GENOME_SERVER_WARNING=false
LAST_TRACK_DIRECTORY=C:\<path_to_dir>
DEFAULT_GENOME_KEY=C:\<path_to_file>

@kunmonster
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@Alan-Collins Glad to see you have solved the problem with my method. Actually I have suspected the problem was caused by the IGV.Bounds too , but I just backuped the "prefs.properties" file and deleted it , it indeed worked. I have also checked that file before and after changes, I found that when the IGV was working , the values of IGV.Bounds were either positive digit or 0, but the values of it when IGV didn't work contained negative values. About the warning , it doesn't affect the use of igv .By the way , warning is not error.

@jrobinso
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jrobinso commented Sep 23, 2024 •
edited
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@Alan-Collins as @kunmonster there are no errors in your log file, those are warnings and all are perfectly normal.

I had thought the problems with IGV.Bounds had been fixed. Leave this issue open and I will see if I can reproduce it when I have some time, which might not be immediately.

@jrobinso jrobinso self-assigned this Sep 23, 2024
@jrobinso jrobinso added this to the 2.19.0 milestone Sep 23, 2024
@kunmonster
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@jrobinso THX， I have tried to reproduce it with changing the values of the IGV.Bounds. But I opened the file and found that the values of the IGV.Bounds invloved negative values when it was wokring perfectly too. So it would not be caused by the negative values. I hope I didn't mislead you about the problem.

This was referenced Sep 27, 2024
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jrobinso pushed a commit that referenced this issue Oct 7, 2024
@kunmonster
Fix issue1512 (#1590)
51ced33 
* add restriction on the values of (x,y),if the value of x is less than -width or the value of y is less than -height,the windows will be hidden.

fixs issue #1512
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@jrobinso @Alan-Collins @kunmonster @projassanchez @palsilva