IGV web app error loading track with cram files

[Zih-Hua Fang]

Dear IGV support,

I would like to report an error I encountered when loading the cram files to IGV web browser. It kept throwing 'Error loading track data' for the read alignments (see attached file). I have tried to load the cram files to the igv web browser with the link of my files in the google bucket, and igv from Terra. The same error was observed. My cram files were validated using GATK ValidateSam. Therefore, I could exclude the issue with the cram files. 

I have also tried to load other cram files from the public google bucket via igv web browser (https://app.terra.bio/#workspaces/anvil-datastorage/1000G-high-coverage-2019/data), which also showed the same error. 

Could anyone help me navigate how to solve the issue?
Thank you in advance.

Best wishes,
Zih-Hua

--
Zih-Hua Fang, PhD
Genome Biology of Neurodegenerative diseases | Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE)
Otfried Müller Strasse 23
72076 Tübingen
Germany

[Zih-Hua Fang]

Here's the screenshot. 

[igv-help]

CRAM files are working in general, but I could not load a "public" cram from the Terra public bucket you reference.   Looking at the network tab in development tools I see this error

"Bucket is requester pays bucket but no user project provided."

Something might have changed in Terra,  please contact them and let us know what they say.    If  a "user project" is required there is a way to specify that in the igv.js API but I do not know if they do that, or not.   

[Fang, Zih-Hua /DZNE]

Hi,

Thanks for getting back to me.

I have already reported to Terra support team.

They can replicate the error both with igv web browser with link and igv on Terra.

They concluded that the issue is with igv since the same error was observed with both igv on Terra and igv web browser, and I was asked to contact igv support.

Here’s the path for a public cram (gs://fc-56ac46ea-efc4-4683-b6d5-6d95bed41c5e/CCDG_13607/Project_CCDG_13607_B01_GRM_WGS.cram.2019-02-06/Sample_HG00096/analysis/HG00096.final.cram)

Index: gs://fc-56ac46ea-efc4-4683-b6d5-6d95bed41c5e/CCDG_13607/Project_CCDG_13607_B01_GRM_WGS.cram.2019-02-06/Sample_HG00096/analysis/HG00096.final.cram.crai

--
Zih-Hua Fang, PhD
Genome Biology of Neurodegenerative diseases | Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE)
Otfried Müller Strasse 23
72076 Tübingen
Germany

Phone: +49 (0)70719254168
Email:  Zih-Hu...@dzne.de
Web: http://www.dzne.de

***********************
Board: Prof. Pierluigi Nicotera, MD PhD (Scientific Director and Chairman of the Executive Board)
and Dr. Sabine Helling-Moegen, LL.M. (Administrative Director).
The DZNE is registered at the associations’ register of the Bonn municipal court (VR 9021).

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/fIQl-uxRUUQ/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/fa42c30f-634b-4673-9427-82395ac20995n%40googlegroups.com.

[igv-help]

I don't know how they can come to that conclusion,  did they look at the network error?   When I try the public cram you reference I get a "400" error from the server with the following error message "Bucket is requester pays bucket but no user project provided.".   Could you please pass this on to them?   Also they "know where to find me (this is Jim)", so they can contact me directly if needed, or open an issue for discussion at https://github.com/igvteam/igv.js.

There's nothing we can do if they have "google pays" turned on.

[Fang, Zih-Hua /DZNE]

Thank you, Jim.

I have forwarded the message to Terra support.

Below is the conversation between Terra support and I to avoid misunderstanding (if there’s any)

====

Given that this issue is being seen with both the IGV web app and IGV within Terra, I'm not sure how much the Terra support team will be able to troubleshoot the problem. Could you please try contacting IGV support with a screenshot of the error you are seeing? We are still trying to solve the problem, but I think the IGV support team may have more insight into what might be going on.

====

--
Zih-Hua Fang, PhD
Genome Biology of Neurodegenerative diseases | Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE)
Otfried Müller Strasse 23
72076 Tübingen
Germany

Phone: +49 (0)70719254168
Email:  Zih-Hu...@dzne.de
Web: http://www.dzne.de

***********************
Board: Prof. Pierluigi Nicotera, MD PhD (Scientific Director and Chairman of the Executive Board)
and Dr. Sabine Helling-Moegen, LL.M. (Administrative Director).
The DZNE is registered at the associations’ register of the Bonn municipal court (VR 9021).

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/a40b71db-1017-4b64-b56c-1cfac43ac536n%40googlegroups.com.

[James Robinson]

OK,   they have "requestor pays" turned on for that public CRAM, so no one is going to be able to load it though the public igv-web.    I don't know if its the same problem for your private CRAMs.

[Fang, Zih-Hua /DZNE]

Hi James,

The same "Error loading track data" error is also occurring with my private CRAMs that are in a private google bucket without requestor pays.

I could load the same crams before without issue. 

--
Zih-Hua Fang, PhD
Genome Biology of Neurodegenerative diseases | Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE)
Otfried Müller Strasse 23
72076 Tübingen
Germany

Phone: +49 (0)70719254168
Email:  Zih-Hu...@dzne.de
Web: http://www.dzne.de

***********************
Board: Prof. Pierluigi Nicotera, MD PhD (Scientific Director and Chairman of the Executive Board)
and Dr. Sabine Helling-Moegen, LL.M. (Administrative Director).
The DZNE is registered at the associations’ register of the Bonn municipal court (VR 9021).

On 26. Jan 2022, at 18:29, James Robinson <jrob...@broadinstitute.org> wrote:

OK,   they have "requestor pays" turned on for that public CRAM, so no one is going to be able to load it though the public igv-web.    I don't know if its the same problem for your private CRAMs.

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/fIQl-uxRUUQ/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BptMNZTqkSKUDYxT-uYYBw0K5o_CH-HC9KiNMrF1UAJVYA%40mail.gmail.com.

[James Robinson]

I can't help with files I can't access, to diagnose, use "development tools" and look for console errors, and also use the "network" tab of development tools to check for errors there.   Network requests that fail will be red.   If IGV hasn't changed and it worked before obviously something else has changed.

If the Terra team think it's an IGV problem, have them open an issue at github.com/igvteam/igv.js/issues with a reproducible test case.    Again we know the problem with the public CRAM you referenced, the bucket is "requestor pays", so that is not a useful test case.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/702FB2C6-E2AD-4A4D-A9AE-A93B4EA3F40F%40dzne.de.