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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