Hi Amit, The problem has to do with the MAF files themselves - they are truncated. This occurs when MAF data is extracted from the Table browser (or any data in excess of ~100k lines). This data greatly exceeds that: *Database:*dm3 *Primary Table:*multiz15way *Row Count:*1,633,505 The ends of both dataset #1 and dataset #3 have this warning: --------------------------------------------------------------------------- procedures have exceeded timeout: 1200 seconds, function has ended. --------------------------------------------------------------------------- Instead, you have two options: 1 - obtain the MAF files from the UCSC downloads area. Go to http://genome.ucsc.edu, then in the left blue side bar select "Downloads", then navigate to the data for dm3. The multiz (MAF) will be under the Conservation track data. 2 - this same MAF data is cashed as a local data source on usegalaxy.org. If you queried the blocks using an interval/bed file of coordinates (assigned with database "dm3"), you could obtain the intervals that way. UCSC has the chromsome names and lengths on the D. Mel home page in a table found by clicking on the link near the top named "Sequences". Simple files from this info can be pasted into the "Get Data -> Upload file" tool form to create one-line query datasets, like this one: I was able to run " Extract MAF blocks" then "MAF to Interval" with no problems. I don't know if doing this one chromosome at time is required, but it certainly will work and not exceed any resources. I suggested doing this once, building a workflow, then running on the rest in batch. Hopefully one of these options works out for you! Jen Galaxy team On 5/16/14 6:59 AM, Amit Pande wrote:
Dear Jennifer,
I uploaded the data both the ways i.e via the FTP and through the UCSC browser, but all the attempts to extract MAF blocks between insect species has failed. I need your help in this regard, so I have shared my history with you. warm regards, Amit.
On Thu, May 15, 2014 at 5:07 PM, Jennifer Jackson <jen@bx.psu.edu <mailto:jen@bx.psu.edu>> wrote:
Hi Amit,
This is occurring when you are uploading a MAF "multizXXway" file obtained from UCSC downloads (genome.ucsc.edu <http://genome.ucsc.edu>) to Galaxy main (usegalaxy.org <http://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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