SV Second Gene Incorrect OncoPrint & Broken Mutation/Download tabs

[Hadyn Tang]

Hi,

 

I’m having trouble importing fusion data into a local cBioPortal instance run on Docker.

 

Specifically, I have followed the following procedure

1. Deploy with Docker via https://docs.cbioportal.org/deployment/docker/, with the only alteration being changing the output ports for firewall purposes.
2. Download the study chol_tcga_pan_can_atlas_2018.
3. Deal with the errors that would be raised if you tried to import the study: delete the gene_panel_matrix file and meta file due to the “panel” WXS being missing, fix incorrect capitalisation in Sample_ID in data_sv.txt and fix missing Site1_Exon/Site2_Exon/Site1_Ensembl_Transcript_Id/Site2_Ensembl_Transcript_Id columns in the same file (by adding empty columns).
4. Import the study.
5. Select study and query a gene that arises as the second gene in a structural variant, such as EFNA2. Expected result: Oncoprint shows one alteration as “Structural Variant (putative drivers)”, and one “Amplification”, as in https://www.cbioportal.org/results/oncoprint?cancer_study_list=chol_tcga_pan_can_atlas_2018&tab_index=tab_visualize&case_set_id=chol_tcga_pan_can_atlas_2018_all&Action=Submit&gene_list=EFNA2. Actual result: only the “Amplification” alteration is visible. Also, an error like the attached file is raised in the docker logs.
6. Select the Mutation tab. Expected result: mutations are visible, as in https://www.cbioportal.org/results/mutations?cancer_study_list=chol_tcga_pan_can_atlas_2018&tab_index=tab_visualize&case_set_id=chol_tcga_pan_can_atlas_2018_all&Action=Submit&gene_list=EFNA2. Actual result: screen goes blank. A similar error is produced in docker logs. Additionally, the console reports “Uncaught (in promise) TypeError: Cannot read properties of undefined (reading 'vus')”.
7. Go back one page, then select the Download tab. Expected result: downloads are visible, as in https://www.cbioportal.org/results/download?cancer_study_list=chol_tcga_pan_can_atlas_2018&tab_index=tab_visualize&case_set_id=chol_tcga_pan_can_atlas_2018_all&Action=Submit&gene_list=EFNA2. Actual result: screen again goes blank. A similar error is produced in docker logs. Additionally, the console reports “Uncaught TypeError: Cannot read properties of undefined (reading 'hugoGeneSymbol')”
8. Go to sample view for a sample with any fusion variant, such as TCGA-3X-AAVA-01. Expected result: In structural variants, the MUM1-EFNA2 fusion is labelled with “Likely oncogenic” from OncoKB, as in https://www.cbioportal.org/patient?sampleId=TCGA-3X-AAVA-01&studyId=chol_tcga_pan_can_atlas_2018. Actual result: a warning triangle appears with “Error fetching OncoKB data”. A similar error is produced in docker logs.

This does not change if I add a private OncoKB license. However, querying a gene which is only found as the first gene in a structural variant (such as, for this study, IRF4) works fine for the gene-related views, although the displayed protein change in the Mutation tab is different from online – locally it displays “MUM1-EFNA2”, which is what’s entered in the Event_Info column, but online it displays as “IRF4-EFNA2 Fusion”.

 

Perhaps this is related to the empty columns for Exons and Ensembl_Transcript_Id, but without them, the file doesn’t even load. (Alternatively, perhaps the issue is the cbioportal docker instance is too new for the currently archived version of the study? But if so, how can this be fixed?)

 

What’s the best way to resolve this issue?

 

Thanks for your assistance!

 

 

Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

[Benjamin Gross]

Hi Hadyn.

Thank you for your thorough description.  I’ve asked one of our data curators to take a look at this study and figure out why you had to make the changes you describe in Step 3.  Once we resolve these, we can see if you still encounter errors analyzing the data.

Sorry for any inconvenience this may have caused.

Regards,

Benjamin

On Jan 24, 2023, at 9:55 PM, 'Hadyn Tang' via cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com> wrote:

Hi,

 

I’m having trouble importing fusion data into a local cBioPortal instance run on Docker.

 

Specifically, I have followed the following procedure

1. Deploy with Docker via https://docs.cbioportal.org/deployment/docker/, with the only alteration being changing the output ports for firewall purposes.
2. Download the study chol_tcga_pan_can_atlas_2018.
3. Deal with the errors that would be raised if you tried to import the study: delete the gene_panel_matrix file and meta file due to the “panel” WXS being missing, fix incorrect capitalisation in Sample_ID in data_sv.txt and fix missing Site1_Exon/Site2_Exon/Site1_Ensembl_Transcript_Id/Site2_Ensembl_Transcript_Id columns in the same file (by adding empty columns).
4. Import the study.
5. Select study and query a gene that arises as the second gene in a structural variant, such as EFNA2. Expected result: Oncoprint shows one alteration as “Structural Variant (putative drivers)”, and one “Amplification”, as in https://www.cbioportal.org/results/oncoprint?cancer_study_list=chol_tcga_pan_can_atlas_2018&tab_index=tab_visualize&case_set_id=chol_tcga_pan_can_atlas_2018_all&Action=Submit&gene_list=EFNA2. Actual result: only the “Amplification” alteration is visible. Also, an error like the attached file is raised in the docker logs.
6. Select the Mutation tab. Expected result: mutations are visible, as in https://www.cbioportal.org/results/mutations?cancer_study_list=chol_tcga_pan_can_atlas_2018&tab_index=tab_visualize&case_set_id=chol_tcga_pan_can_atlas_2018_all&Action=Submit&gene_list=EFNA2. Actual result: screen goes blank. A similar error is produced in docker logs. Additionally, the console reports “Uncaught (in promise) TypeError: Cannot read properties of undefined (reading 'vus')”.

1. Go back one page, then select the Download tab. Expected result: downloads are visible, as inhttps://www.cbioportal.org/results/download?cancer_study_list=chol_tcga_pan_can_atlas_2018&tab_index=tab_visualize&case_set_id=chol_tcga_pan_can_atlas_2018_all&Action=Submit&gene_list=EFNA2. Actual result: screen again goes blank. A similar error is produced in docker logs. Additionally, the console reports “Uncaught TypeError: Cannot read properties of undefined (reading 'hugoGeneSymbol')”

1. Go to sample view for a sample with any fusion variant, such as TCGA-3X-AAVA-01. Expected result: In structural variants, the MUM1-EFNA2 fusion is labelled with “Likely oncogenic” from OncoKB, as in https://www.cbioportal.org/patient?sampleId=TCGA-3X-AAVA-01&studyId=chol_tcga_pan_can_atlas_2018. Actual result: a warning triangle appears with “Error fetching OncoKB data”. A similar error is produced in docker logs.

This does not change if I add a private OncoKB license. However, querying a gene which is only found as the first gene in a structural variant (such as, for this study, IRF4) works fine for the gene-related views, although the displayed protein change in the Mutation tab is different from online – locally it displays “MUM1-EFNA2”, which is what’s entered in the Event_Info column, but online it displays as “IRF4-EFNA2 Fusion”.

 

Perhaps this is related to the empty columns for Exons and Ensembl_Transcript_Id, but without them, the file doesn’t even load. (Alternatively, perhaps the issue is the cbioportal docker instance is too new for the currently archived version of the study? But if so, how can this be fixed?)

 

What’s the best way to resolve this issue? 

 

Thanks for your assistance!

 

 

Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt. 

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<chol_error.txt>

[Hadyn Tang]

Dear Benjamin,

 

Thank you very much for your swift response! That would be great, and no worries about the inconvenience – it’s just amazing that a tool like cBioPortal exists at all. is open source and has such a helpful community.

Kind regards,

Hadyn

 

From: Benjamin Gross <benjami...@gmail.com>
Sent: Thursday, 26 January 2023 12:17
To: Hadyn Tang <Hadyn...@petermac.org>; Satravada, Baby A./Sloan Kettering Institute <satr...@mskcc.org>
Cc: cbiop...@googlegroups.com
Subject: Re: [cbioportal] SV Second Gene Incorrect OncoPrint & Broken Mutation/Download tabs

 

! EXTERNAL EMAIL: Think before you click. If suspicious send to Cyber...@petermac.org

[Satr...@mskcc.org]

Hi Hadyn,

It looks like you are using an older version of cbioportal docker instance. Can you try updating your local cBioPortal docker container using this command (# docker pull cbioportal/cbioportal:latest) and then try importing the study. If that doesn’t work you can also try using the latest development version. 

That is change:

 https://github.com/cBioPortal/cbioportal-docker-compose/blob/master/.env#L1

to cbioportal/cbioportal:5.2.5

I tried importing from our end and the study got imported without any issues. 

Hope that helps!

Best wishes,

Baby Anusha.

---

From: Benjamin Gross <benjami...@gmail.com>
Sent: Wednesday, January 25, 2023 8:17 PM
To: Hadyn Tang <Hadyn...@petermac.org>; Satravada, Baby A./Sloan Kettering Institute <Satr...@mskcc.org>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: [EXTERNAL] Re: [cbioportal] SV Second Gene Incorrect OncoPrint & Broken Mutation/Download tabs

 

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[Hadyn Tang]

Dear Baby Anusha,

 

Thanks for your help! Unfortunately I got an error about the JVM running out of memory for the 5.2.5 version (even after changing -Xmx and -Xms), but I’ll try to see first whether that may just be an issue with the server it is being run on.

 

Kind regards,

Hadyn

 

From: "Satr...@mskcc.org" <satr...@mskcc.org>
Date: Friday, 27 January 2023 at 5:28 am
To: "benjami...@gmail.com" <benjami...@gmail.com>, Hadyn Tang <Hadyn...@petermac.org>
Cc: "cbiop...@googlegroups.com" <cbiop...@googlegroups.com>
Subject: Re: Re: [cbioportal] SV Second Gene Incorrect OncoPrint & Broken Mutation/Download tabs

 

! EXTERNAL EMAIL: Think before you click. If suspicious send to Cyber...@petermac.org

Hi Hadyn,

[Gaofei Zhao]

Hi Hadyn,

Just wanted to check in to see if you solved the JVM out-of-memory issue. Normally it's just related to the  -Xmx and -Xms settings. If you are still facing this issue, I can help you debug this issue.

Sincerely,

Gaofei

[Hadyn Tang]

Hi,

 

Sorry for the repeated issues, but after trying multiple times to get version 5.2.5 to run, I haven’t been able to resolve the JVM issue. (Simply pulling the latest image didn’t actually change anything.)

 

The error log is as attached. Also, if it helps, the server specs are:

• RAM: 32 GB
• VCPUs: 8
• Disk: 30 GB

As I mentioned, I already tried increasing (and decreasing) -Xmx and -Xms in the command in docker-compose.yml, but that didn’t have any noticeable effect.

 

Is this a known issue that I need to take some steps to mitigate, or possibly an issue caused by having some older installation lingering around on the same system for some reason? (I did clear the previous containers, volumes and images before making the switch, but perhaps there is some inconsistency with some of the other containers like the versions of MongoDB or MySQL.)

 

Kind regards,

Hadyn