Question: MegaBLAST Output: How to get WHAT and TAXON??
gravatar for mjmv
4.3 years ago by
United States
mjmv0 wrote:

The results of the BLAST do not seem to include detailed information about WHAT and in which TAXON the hit was to.

Is there a way to quickly get this information for all with significant E-values?




galaxy • 856 views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by mjmv0
gravatar for Jennifer Hillman Jackson
4.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


If you are working on the public Main Galaxy instance at http://usegalaxy,org. please see the taxonomy tools under the group "Metagenomic analyses". If you want to filter first, or cut columns, join datasets together, or otherwise customize your workflow, see the tools in the groups "Text Manipulation", "Filter and Sort", and "Join, Subtract, Group" - all work well on tabular datasets.

If on a local/local Galaxy, these same tools are in the Tool Shed and can be installed for use: http://usegalaxy,org/toolshed

If on another public Galaxy, the available tools can vary. Manipulation tools are generally standard, Metagenomic tools may or may not be included. If not, move to an alternative (Main, local or cloud).

Best, Jen, Galaxy team

ADD COMMENTlink written 4.3 years ago by Jennifer Hillman Jackson25k

The output from the Megablast feature does not label the columns.  Is this why it does not want to feed into the Fetch Taxonomic Representation tool?  Column 1 is the sequence, and 2 the NCBI sequence ID number.  However, the tool is saying there is an error with how these columns are being identified.

ADD REPLYlink written 4.3 years ago by mjmv0

This is a strange occurrence. I have only seen this come up when the tool is launched prior to the Megablast job completing. In these cases, the columns are not in a pull-down option on the tool form, but rather input boxes appear where one can then enter the column numbers. Using the correct nomenclature - "c1" and "c2" will usually do the trick. However, I have seen these then become translated to "1" and "2", and therefore become invalid input, in certain cases.

Is this the tool behavior you are experiencing? Do you have a history that you can share with me (privately) that demonstrates this usage and behavior? If it is noticeable to others besides myself (no one else has brought this up before, is just something I have encountered myself, and not consistently), I believe it should be remedied, or at least reviewed, and would like to open a ticket in Trello.

To share a history, create a share link using the history menu, copy it, and email to (internal to our core team, so has data privacy). Please include the user name from this post so I can link the two together. We can post the remedy/resolution and/or any tickets opened back here, but without any private data/details. 

Should the issue be different than the one I am explaining here, then definitely share a history and we can figure out what is going on. If you are not on the public Main instance, testing if this is reproducible there will aid in diagnosing the issue, so is worth doing. Just use a small sample dataset to have the runs go quickly.

Thanks! Jen, Galaxy team

ADD REPLYlink written 4.3 years ago by Jennifer Hillman Jackson25k

Thank you for sharing the history. For very large datasets, the "Fetch taxonomic representation" tool is (incorrectly) presenting warnings on the tool form. Ignore these and execute the job anyway. In my testing, with your exact dataset, results were successful. (I also did some other format checks - everything in the input is fine). A Trello ticket to address this has been opened here:

It will be possible to submit a dataset that is simply too large for the tool to run on (given any Galaxy instance's particular resources), but that is a different use-case, and would result in an error reported after execution, not warnings before. 

Thank you for the follow up! Take care, Jen, Galaxy team

ADD REPLYlink written 4.3 years ago by Jennifer Hillman Jackson25k
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