Hi Amit,

This is occurring when you are uploading a MAF "multizXXway" file obtained from UCSC downloads (genome.ucsc.edu) to Galaxy main (usegalaxy.org)? Upload using FTP? https://wiki.galaxyproject.org/Support#Loading_data


The table browser is generally a poor choice to extract more than a few regions with MAF data (per query) as there are limits on how many lines of output will be sent over. Incomplete transfers are a common. This error could be related to a format or datatype assignment issue from that type of issue.

Please give FTP loading a try if you have not already. Then if problems continue, you can share a history link with me. Note which dataset was the MAF uploaded via FTP. This is how to share: https://wiki.galaxyproject.org/Learn/Share

Best,

Jen
Galaxy team

Going forward, please ask questions on our new forum that is replacing this list (very soon now):
https://wiki.galaxyproject.org/Support#Biostar

On 5/14/14 10:52 PM, Amit Pande wrote:
Dear Galaxy,

I am trying to import a multiz alignment file for all the insect species from the UCSC
genome browser.
Galaxy does not recognize number of blocks in the multiz file as there is a question mark in the file format view (? blocks). Then when I am trying to use the tool ( Extract MAF blocks <https://usegalaxy.org/tool_runner?tool_id=Interval2Maf1> given a set of genomic intervals) then there is an error saying

"An error occurred with this dataset:191757 MAF blocks converted to Genomic Intervals for species dm3. There was a problem processing your input: exceptions must be old-style classes or derived from BaseException, not str" and even when the tool runs it shows the following message "
This is a new dataset and not all of its data are available yet "

Please look into the problem.

warm regards,
Amit.


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___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
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Posts to this list will be disabled in May 2014.  In the
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