Error loading features

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Débora Parrine

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Nov 27, 2020, 8:51:11 AM11/27/20
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Hi,

I have been seen this error constantly when navigating (zooning in or out) the tracks:

ERROR [2020-11-27T14:45:17,775] [FeatureTrack.java:739]  Error loading features for interval: chr1:0-197195432 <br>java.lang.NullPointerException
java.lang.NullPointerException: null
at org.broad.igv.track.FeatureTrack.loadFeatures(FeatureTrack.java:722) [igv.jar:?]
at org.broad.igv.track.FeatureTrack.load(FeatureTrack.java:691) [igv.jar:?]
at org.broad.igv.ui.IGV.lambda$repaint$8(IGV.java:2389) [igv.jar:?]
at java.util.concurrent.CompletableFuture$AsyncRun.run(Unknown Source) [?:?]
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [?:?]
at java.lang.Thread.run(Unknown Source) [?:?]

after the error is displayed, the tracks disappear.

Yu Tao

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Jan 12, 2021, 5:05:37 PM1/12/21
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I also have the same problem and could not figure out the reason.

I prepared saved session and when open it, it shows such error. I supposed it is because of the constant upgrading of the ref. genome in IGV automatically. But even I used a saved version of ref. genome in my computer, this problem continues to occur.

Could anyone help on this?

Best
Zutao 

jrob...@broadinstitute.org

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Jan 12, 2021, 6:28:57 PM1/12/21
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Its difficult to help with such minimal information.    See the welcome message for this group (https://groups.google.com/u/1/g/igv-help) for the type of information we generally need for diagnosis. 
Message has been deleted

Jiri Macas

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Apr 13, 2021, 4:08:08 AM4/13/21
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I have found that in my case the problem was caused by using relative paths for track file locations. After disabling this option (in View -> Preferences -> General: Use relative path in session files) the file locations were saved using absolute paths and everything worked fine.

Jiri

On Monday, April 12, 2021 at 10:34:12 AM UTC+2 Jiri Macas wrote:
Hi,

I have the same problem with IGV 2.9.2 run on Ubuntu 18.04 (32 GB RAM).  When I upload gff3 annotation tracks to a genome and save the session, the error appears after re-opening the session. Below is the corresponding info from "igv.log".

Thanks,   Jiri

--------
INFO [2021-04-12T10:28:57,352] [Main.java:205]  Startup  IGV Version 2.9.4 03/17/2021 05:06 PM
INFO [2021-04-12T10:28:57,359] [Main.java:206]  Java 11.0.10 (build 11.0.10+9) 2021-01-19
INFO [2021-04-12T10:28:57,360] [Main.java:209]  Java Vendor: AdoptOpenJDK https://adoptopenjdk.net/
INFO [2021-04-12T10:28:57,360] [Main.java:211]  JVM: OpenJDK 64-Bit Server VM AdoptOpenJDK   
INFO [2021-04-12T10:28:57,387] [Main.java:214]  Default User Directory: /home/jirka
INFO [2021-04-12T10:28:57,387] [Main.java:215]  OS: Linux 4.15.0-140-generic amd64
INFO [2021-04-12T10:28:57,900] [GenomeManager.java:183]  Loading genome: /mnt/raid/454_data/MinION/analysis/centromere_assembly_Cameor/210304_CEN6_all_scaff_and_assembly/all_scaff_210305/igv/CEN6_all_scaff_210305.genome
INFO [2021-04-12T10:28:58,122] [CommandListener.java:121]  Listening on port 60151
INFO [2021-04-12T10:29:36,094] [IGV.java:1316]  Loading 2 resources.
INFO [2021-04-12T10:29:36,102] [TrackLoader.java:122]  Loading resource, path /mnt/raid/454_data/MinION/analysis/centromere_assembly_Cameor/210304_CEN6_all_scaff_and_assembly/all_scaff_210305/repeatmasker_SAT/RM/FabTR-10_cutoff_1kb_track.gff3
INFO [2021-04-12T10:29:36,145] [TrackLoader.java:122]  Loading resource, path /mnt/raid/454_data/MinION/analysis/centromere_assembly_Cameor/210304_CEN6_all_scaff_and_assembly/all_scaff_210305/repeatmasker_SAT/RM/FabTR-48_cutoff_1kb_track.gff3
INFO [2021-04-12T10:30:08,498] [ShutdownThread.java:47]  Shutting down
INFO [2021-04-12T10:30:32,242] [Main.java:205]  Startup  IGV Version 2.9.4 03/17/2021 05:06 PM
INFO [2021-04-12T10:30:32,251] [Main.java:206]  Java 11.0.10 (build 11.0.10+9) 2021-01-19
INFO [2021-04-12T10:30:32,252] [Main.java:209]  Java Vendor: AdoptOpenJDK https://adoptopenjdk.net/
INFO [2021-04-12T10:30:32,253] [Main.java:211]  JVM: OpenJDK 64-Bit Server VM AdoptOpenJDK   
INFO [2021-04-12T10:30:32,287] [Main.java:214]  Default User Directory: /home/jirka
INFO [2021-04-12T10:30:32,288] [Main.java:215]  OS: Linux 4.15.0-140-generic amd64
INFO [2021-04-12T10:30:32,835] [GenomeManager.java:183]  Loading genome: /mnt/raid/454_data/MinION/analysis/centromere_assembly_Cameor/210304_CEN6_all_scaff_and_assembly/all_scaff_210305/igv/CEN6_all_scaff_210305.genome
INFO [2021-04-12T10:30:33,043] [CommandListener.java:121]  Listening on port 60151
INFO [2021-04-12T10:30:47,229] [TrackLoader.java:122]  Loading resource, path /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/210304_CEN6_all_scaff_and_assembly/all_scaff_210305/repeatmasker_SAT/RM/FabTR-10_cutoff_1kb_track.gff3
INFO [2021-04-12T10:30:47,229] [TrackLoader.java:122]  Loading resource, path /mnt/ceph/454_data/MinION/analysis/centromere_assembly_Cameor/210304_CEN6_all_scaff_and_assembly/all_scaff_210305/repeatmasker_SAT/RM/FabTR-48_cutoff_1kb_track.gff3
INFO [2021-04-12T10:30:47,347] [MessageUtils.java:76]  Error loading features for interval: scaff_1722_ver_2:0-10197491 <br>java.lang.NullPointerException
INFO [2021-04-12T10:30:47,347] [MessageUtils.java:76]  Error loading features for interval: scaff_1722_ver_2:0-10197491 <br>java.lang.NullPointerException
ERROR [2021-04-12T10:30:52,276] [FeatureTrack.java:739]  Error loading features for interval: scaff_1722_ver_2:0-10197491 <br>java.lang.NullPointerException
java.lang.NullPointerException: null
at org.broad.igv.track.FeatureTrack.loadFeatures(FeatureTrack.java:722) [igv.jar:?]
at org.broad.igv.track.FeatureTrack.load(FeatureTrack.java:691) [igv.jar:?]
at org.broad.igv.ui.IGV.lambda$repaint$12(IGV.java:2426) [igv.jar:?]
at java.util.concurrent.CompletableFuture$AsyncRun.run(Unknown Source) [?:?]
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [?:?]
at java.lang.Thread.run(Unknown Source) [?:?]
ERROR [2021-04-12T10:30:53,056] [FeatureTrack.java:739]  Error loading features for interval: scaff_1722_ver_2:0-10197491 <br>java.lang.NullPointerException
java.lang.NullPointerException: null
at org.broad.igv.track.FeatureTrack.loadFeatures(FeatureTrack.java:722) [igv.jar:?]
at org.broad.igv.track.FeatureTrack.load(FeatureTrack.java:691) [igv.jar:?]
at org.broad.igv.ui.IGV.lambda$repaint$12(IGV.java:2426) [igv.jar:?]
at java.util.concurrent.CompletableFuture$AsyncRun.run(Unknown Source) [?:?]
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [?:?]
at java.lang.Thread.run(Unknown Source) [?:?]
INFO [2021-04-12T10:31:08,642] [ShutdownThread.java:47]  Shutting down
----------------------------

Helga Thorvaldsdottir

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Apr 13, 2021, 3:28:51 PM4/13/21
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Hi Jiri - thanks for letting us know.

Helga

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