Buffer overflow errors when uploading trackhubs of bigbeds

[Jake Yeung]

Hello UCSC browser experts.

I am trying to visualize some bigbed files using trackhubs. The individual bigbeds work when I upload them as custom tracks. However, when I put all bigbeds into a trackhub, I get the following error:

buffer overflow, size 2, format %s, buffer ‘(‘

(screenshot below)

Do you guys have any ideas of how this error could arise?

Thanks in advance,

Jake

[Cath Tyner]

Hello Jake,

Thanks for contacting the UCSC Genome Browser support team

​, and thank you so much for including a screen shot of your issue. 

​

In order to best provide troubleshooting assistance, would you be willing to share your trackDb.txt so that we can examine the details? If you prefer, you can send this directly to me rather than including the mailing list

​ on your email response. ​

​

Meanwhile, ​

​Can you

 check for an unexpected "(...)" in the strand column

​?​

Can you also let me know 

how many fields of BED your rows start with

​?

Once we have more information, we can take a closer look and hopefully provide suggestions for fixing this issue.

Thank you for contacting the UCSC Genome Browser support team. 

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mail 

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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[Christopher Lee]

Hi Jake,

Thank you for your question about buffer overflows when loading your track hub. It appears that some lines of your bigBed files don't contain a strand column, and thus are not valid bigBed 6 files, which is causing the errors you are seeing.

We also recommend using the hubCheck utility (available here: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/hubCheck) in order to check the tracks in your hubs.

If you modify your bigBed files so they are valid bed 6 files your hub should work.

Please let us know if you have any further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
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you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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