Thank you Jeremy,

It turned out the issue was our version of bedtools. We updated to 2.17.0 and no longer have the errors.


From:        Jeremy Goecks <>
To:        Liisa Koski <>
Cc:        " Galaxy-dev" <>
Date:        05/10/2013 08:08 PM
Subject:        Re: [galaxy-dev] Visualizations broken after Aug. 12 update

You'll need to do two things:

(1) Install wigToBigWig and bedtools; see steps 2 and 3 here:

(2) Update your datatypes_conf.xml file:

If you haven't made changes to your datatypes_conf.xml file, you can just copy datatypes_conf.xml.sample to datatypes_conf.xml to get the needed converters.

If you've made changes to datatypes_conf.xml, you'll need to manually add the needed converters. We recently transitioned all the *_to_summary_tree converters to *_to_bigwig, so you'll want to remove the summary_tree converters and replace them with the bigwig converters.

Let us know if you have any problems/questions.


On Oct 3, 2013, at 1:33 PM, Liisa Koski wrote:

We recently updated to the Aug.12 distribution. I u commented the visualizations_config_directory = config/visualizations in the universe file and when I restarted and tried to view past Trackster Visualizations none of my tracks load. I get the error displayed in the track itself:

Cannot display dataset due to an error. View error. Try again.

When I click on View error I get pop up with this for my gff3 track:

Input error: Cannot split into blocks. Found interval with fewer than 12 columns.
needLargeMem: trying to allocate 0 bytes (limit: 17179869184)

With this for my BAM track:

grep: /Galaxy/galaxy_dist/database/files/016/dataset_16392.dat: No such file or directory
needLargeMem: trying to allocate 0 bytes (limit: 17179869184)

All tracks in all published Visualizations are no longer loading.

I do not see any errors in the log files.

I have also updated my datatypes.conf file by copying over datatypes.conf.sample

Any help would be much appreciated.

Thanks in advance,


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