Can't load my sequence

Karl Krueger

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Oct 15, 2025, 5:07:03 PMOct 15

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I'm using version 2.9.4 on a Win 11 PC. IGV no longer can open my cram file. When I tell it any gene I want to look at I get a constant hour glass. It's like its trying to get the sequence but can't.

When I had started up IGV today it downloaded something upon start up but now it does not work work for me.

igv-help

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Oct 16, 2025, 12:14:00 PMOct 16

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- Can you confirm that the reference genome you've selected in IGV is the same as the one used to align the cram file?

- Does the problem only occur when you enter a gene name? What about if you enter a specific genomic locus eg chr12:25,356,180-25,405,863 ?

- There might be useful information in the IGV log from the run of IGV that is failing. Can you share it with us? The log is in the "igv" folder under your user home folder. The file is named igv0.log or perhaps igv1.log depending on how much you've run IGV.

Karl Krueger

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Oct 22, 2025, 7:04:20 PMOct 22

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Sorry for not getting back earlier. It seems the problem was somehow my installed IGV got corrupted. I downloaded the latest version and that works fine.

Karl

igv-help

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Oct 23, 2025, 11:29:24 AMOct 23

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No problem. Thanks, for letting us know.

Helga

Karl Krueger

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Oct 29, 2025, 8:00:58 AMOct 29

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This problem just showed up again with the latest downloaded IGV I have (2.19.6). It leaves room for the track of my CRAM file but it will not show the data. When I first started IGV an error message showed up that I couldn't read completely because the message only stayed up for 2 seconds. It said something like it could not read some file???? Shutting down IGV and restarting does not help. It seems to load hg38 fine and when I tell it what gene I want to look at the lower track shows the gene structure - it just does nothing with my own data.

So it looks like this could be a recurring problem for me? Is there a fix I can use when it happens or should I just reinstall IGV again?

Karl

Karl Krueger

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Oct 29, 2025, 8:10:20 AMOct 29

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I just uninstalled and reinstalled 2.19.7 This is working so far. This makes me wonder will this be a recurring problem for me. Is there anything I should pay particular attention when trouble shooting this?

Karl

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