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Loading human/mouse bam files stopped working #309

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assaron opened this issue Jan 17, 2025 · 6 comments
Open

Loading human/mouse bam files stopped working #309

assaron opened this issue Jan 17, 2025 · 6 comments

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@assaron
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assaron commented Jan 17, 2025

I have troubles loading a bam file, which worked previously.

Steps to reproduce:

  1. Open https://igv.org/app/
  2. Load bam file from https://drive.google.com/file/d/1n5QuNd_rAOfDCDPCwi5rc_-J6a2dgTyb/view?usp=drive_link and bai file from https://drive.google.com/file/d/1SUSi6LuGcsVUkZHxPPckDMSRa3AbaABj/view?usp=drive_link

Expect bam track to load, but nothing happens.

Here is the log from Firefox JS console:

XML Parsing Error: syntax error
Location: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes
Line Number 1, Column 1: [hg38.chrom.sizes:1:1](https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes)
Source map error: Error: URL constructor:  is not a valid URL.
Resource URL: wasm:https://igv.org/app/app_bundle-2.1.3.js%20line%2056%20%3E%20WebAssembly.Module
Source Map URL: null

Error: Genome requires either a single JSON file, UCSC hub.txt file, genbank ".gbk" file, or a FASTA & index file
    loadPaths https://igv.org/app/app_bundle-2.1.3.js:10656
    FileLoad https://igv.org/app/app_bundle-2.1.3.js:9040
    FileLoad https://igv.org/app/app_bundle-2.1.3.js:9035
    GenomeFileLoad https://igv.org/app/app_bundle-2.1.3.js:10619
    initializationHelper https://igv.org/app/app_bundle-2.1.3.js:12657
    main https://igv.org/app/app_bundle-2.1.3.js:12604
    async* https://igv.org/app/app_bundle-2.1.3.js:12451
    EventListener.handleEvent* https://igv.org/app/app_bundle-2.1.3.js:12451
    <anonymous> https://igv.org/app/app_bundle-2.1.3.js:4
    <anonymous> https://igv.org/app/app_bundle-2.1.3.js:5
@jrobinso
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Are you trying to load a bam file from the "Genome" menu?

@assaron
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assaron commented Jan 17, 2025

Yes, sorry. I load from local files using Genome/Local file... menu. For hg38 genome (the default one).

@jrobinso
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The Genome menu is for loading genome definitions, use the Tracks menu to load tracks such as bam files.

@assaron
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assaron commented Jan 17, 2025

Hah, that make sense, my bad!

I think what threw me off guard was that there was no changes and no errors, when I mistakenly did this. Could be nice to show an error to user that they are not loading a genome file.

@assaron assaron closed this as completed Jan 17, 2025
@helgathorv
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It used to issue an error in that case. We'll look into that.

@turner turner reopened this Jan 17, 2025
@turner
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turner commented Jan 17, 2025

I will look into why the error dialog does not appear.

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4 participants