Error reading zoom level data records (Table O)

[Benjamin Story]

I have 6 BigWig files (.bw) each representing either the plus or minus strand of 3 biological replicates (the controls). For the past two months they have been loading fine in IGV (opened  fine multiple occasions in Jan and Feb, verified working last Tuesday)

However, starting yesterday I get the error: "Error reading zoom level data records (Table O)" for 2 out of the 6 files (control_1_minus_strand and control_2_plus_strand).

Any ideas on what I might do to rectify this situation and re-enable the loading of these two files? 

Perhaps I may have altered some of my settings in IGV or something?

Help would be greatly appreciated.

[Jim Robinson]

Hi,

What exact version of IGV are you using (do Help > About and read the full version from the dialog).   Could you send us an example bigwig, or post it somewhere where can download it, that replicates the problem?  You can send it to igv-...@broadinstitute.org.

Jim

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[Benjamin Story]

Hey Jim,

Thanks for the quick response. I'm was using the following version of IGV:

Version 2.3.25 (29)

11/25/2013 11:20 AM

Anyway, I just downloaded the newer version (2.3.31) and the two files are now loading properly. Thanks for the help!

Best,

Ben

[riccardo...@gmail.com]

Hello everyone.
I am experiencing the same problem: I have a BigWig file that, until yesterday, were loading perfectly in IGV.
However now I get the error "Error reading zoom level data records (Table O)" and the file is not loaded.

The file I am loading is a BigWig representing reads aligned on the horse genome, from a ChIP seq experiment (size about 180 Mb).
I am using version 2.3.32 (37).
Any ideas on the problem?
Could it be a matter of memory?
I'll greatly appreciate any help.

[James Robinson]

Hi Ricardo,

Its strange that it loaded before yesterday because IGV has not been touched in several months.   Is it possible to make this file available?   I can post anonymous ftp instructions.

Jim

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[riccardo...@gmail.com]

Yes I would like to make the file available. I tried attaching it to the message but I guess it is too big.

[riccardo...@gmail.com]

Also: I can visualize the file on UCSC genome browser, and everything seems to be fine. I don't think it's broken or something like that.
Thank you

[James Robinson]

Hi,

You can upload it by ftp following the instructions below.   Once uploaded either reply here,  or email igv-team (at) broadinstitute.org so I know its there.

"Our external public ftp site address is ftp.broadinstitute.org. A user logs in with a username of anonymous and a password of their email address.

Once connected, the user can upload the data to the incoming directory  (note:  "cd incoming"). This upload directory is a blind directory, i.e. after the upload is done, the file that was uploaded, or any file in the incoming directory, cannot be read."

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/fdb1ed60-adf1-4eec-98b9-74e046a74be0%40googlegroups.com.

[riccardo.gamba89]

Hey,
I think I just uploaded the file to your directory. The file name is "Riccardo_Horse".

Let me know if you see that.

I really hope you can help me, thank you a lot for your time.

Riccardo

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[James Robinson]

Hi Riccardo,

This file appears to be corrupt, or at the very least cannot be read with UCSC tools (see the error below).  Are you sure this file was successfully read earlier?  Do you have the original wig file?  If so I would try re-creating the bigwig.

~/bin/ucscUtils/bigWigToWig Riccardo_Horse.bigwig Riccardo_Horse.wig

udc couldn't read 4 bytes from Riccardo_Horse.bigwig, did read 0

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