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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Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/
Posts to this list will be disabled in May 2014. In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.
For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
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