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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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Error Message after installing 2.18 version in windows. Error "Cannot invoke 'Java.io.bufferedreader.close()' because reader is null" #1552

Open Jeevankumar404346 opened 2 months ago

Jeevankumar404346 commented 2 months ago

Dear team,

We tried installing the packaging using the below link and after completion of installation, getting error message as shown in the below screenshot. Could you please help to fix the issue.

https://data.broadinstitute.org/igv/projects/downloads/2.18/IGV_Win_2.18.2-WithJava-installer.exe

Error Message after installing 2.18 version. Error "Cannot invoke 'Java.io.bufferedreader.close()' because reader is null"

Jeevankumar404346 commented 2 months ago

I am not able to download the file, is it a fix to the issue reported. can you confirm it.

jrobinso commented 2 months ago

@Jeevankumar404346 I do not understand your comment, download what file?

There might be more information in your igv log file, located in the folder /igv. The filename is usually "igv0.log". It should show the stack trace which might help us identify the issue. Can you zip and attach the log, or paste the stack trace here? If it contains sensitive information you can email it to igv-team@broadinstitute.org.

Jeevankumar404346 commented 2 months ago

igv0.log attached the log file. Please check and advise

jrobinso commented 2 months ago

Is it possible you have a firewall or proxy blocking access to https://igv-genepattern-org.s3.amazonaws.com/genomes/hg38/hg38.json?

jbelsky commented 2 months ago

Hi, can confirm I am running into the same issue with hg19 on IGV 2.17.4. When I try to put the url in the browser I'm getting an Access Denied.

INFO [Sep 03,2024 14:19] [GenomeManager] Loading genome: https://s3.amazonaws.com/igv.org.genomes/hg19/hg19.json
SEVERE [Sep 03,2024 14:19] [MessageUtils] Error loading genome: hg19
SEVERE [Sep 03,2024 14:19] [MessageUtils] java.lang.NullPointerException: Cannot invoke "java.io.BufferedReader.close()" because "reader" is null
    at org.igv/org.broad.igv.feature.genome.load.JsonGenomeLoader.loadGenome(JsonGenomeLoader.java:72)
    at org.igv/org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:197)
    at org.igv/org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:171)
    at org.igv/org.broad.igv.ui.IGV$StartupRunnable.run(IGV.java:1933)
    at org.igv/org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)

SEVERE [Sep 03,2024 14:19] [MessageUtils] Error loading genome: hg19
helgathorv commented 2 months ago

@jbelsky There was an issue with the AWS bucket. It has been resolved now.