Error Loading Wig Tracks

[Brew Belly]

IGV version = 2.17.3

I had a saved, properly working tnSeq session with several tracks. I had to reboot and then after reopening the session IGV failed to display the insertion counts (wiggle) tracks (they were just flat lines). I started a new session, beginning with loading a custom genome (fasta and fai) - that diplays the chrom name and sequence OK. 

Trying to load my wiggle files still fails (they 'load' but have no bars for the data). 

The wiggle header reads:

track type=wiggle_0
variableStep chrom=BW30270_norm.fasta
29 50
46 0
64 8
83 2
96 7
101 0

[igv-help]

Can you try IGV version 2.17.4 and see if it behaves the same way.

And if it does, can you share with us the log from the IGV run (you'll find the IGV log file in igv folder in your home folder. It will be named something like igv0.log (or igv1.log etc).

[igv-help]

Also verify that the sequence name in your fasta file is "BW30270_norm.fasta".     Another thing to check is the data scale for the track.   A screenshot might help here.

[Brew Belly]

Thanks for the suggestions.  I installed 2.17.4, same issue. 

The chrom name in the wig matches the loaded chrom name.

The scale seems OK, is set to 10 here, but highest data are 50.

screen shot:

can't find way to upload log file as attachment, so here is the end of it:

INFO [Apr 02,2024 09:15] [TrackLoader] Loading resource:  /Users/Sean/Desktop/Sean Lab Meetings/wcaM_TnSeq_Galaxy/Cap read counts of BW for HMM/WT capped 50 with BW30270_norm.wig
INFO [Apr 02,2024 09:20] [TrackLoader] Loading resource:  /Users/Sean/Desktop/Sean Lab Meetings/wcaM_TnSeq_Galaxy/Cap read counts of BW for HMM/WT capped 50 with BW30270_norm.wig
INFO [Apr 02,2024 09:31] [TrackLoader] Loading resource:  /Users/Sean/Desktop/Sean Lab Meetings/wcaM_TnSeq_Galaxy/WcaM Galaxy Downloads/BW30270_map/BW TA sites.wig
INFO [Apr 03,2024 09:13] [ShutdownThread] Shutting down
INFO [Apr 03,2024 09:14] [Main] Startup  IGV Version 2.17.4 03/23/2024 09:32 PM
INFO [Apr 03,2024 09:14] [Main] Java 17.0.9 (build 17.0.9+9) 2023-10-17
INFO [Apr 03,2024 09:14] [Main] Java Vendor: Eclipse Adoptium https://adoptium.net/
INFO [Apr 03,2024 09:14] [Main] JVM: OpenJDK 64-Bit Server VM Temurin-17.0.9+9  
INFO [Apr 03,2024 09:14] [Main] OS: Mac OS X 13.4.1 x86_64
INFO [Apr 03,2024 09:14] [Main] IGV Directory: /Users/Sean/igv
INFO [Apr 03,2024 09:14] [Main] Resoluction scale = 0.0
INFO [Apr 03,2024 09:14] [CommandListener] Listening on port 60151
INFO [Apr 03,2024 09:14] [GenomeManager] Loading genome: /Users/Sean/Desktop/Sean Lab Meetings/wcaM_TnSeq_Galaxy/BW30270_v3 genome reference/BW30270 normalized and fai indexed/BW30270_norm.fasta
WARNING [Apr 03,2024 09:14] [LoadFromServerAction] No data found for current genome.
INFO [Apr 03,2024 09:15] [GenomeManager] Loading genome: /Users/Sean/Desktop/Sean Lab Meetings/wcaM_TnSeq_Galaxy/BW30270_v3 genome reference/BW30270 normalized and fai indexed/BW30270_norm.fasta
WARNING [Apr 03,2024 09:15] [LoadFromServerAction] No data found for current genome.
INFO [Apr 03,2024 12:09] [TrackLoader] Loading resource:  /Users/Sean/Desktop/Sean Lab Meetings/wcaM_TnSeq_Galaxy/Cap read counts of BW for HMM/WT capped 50 with BW30270_norm.wig

[James Robinson]

Your screenshot indicates a fasta sequence name of "BW30270i",  however the wig variable step line in your snippet has a sequence name of "BW30270_norm.fasta".   

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