hello,

I've run across a possible bug in ODoSE that is preventing me from analyzing my 
data.  I've scoured the various help documentation without luck, so I'm writing 
you. 

I'm using the program via this site: 
http://www.odose.nl/

The history showing the steps below is here: 

http://www.odose.nl/u/publ/h/unnamed-history

The problem is this: I'm unable to work with a set of genomes that is 
exclusively "user-generated" (i.e., external, and uploaded from my local 
drive). 

To illustrate this problem with an example, I downloaded the .ffn files for 
four published genomes NCBI's ftp site.  (This way, I'm sure my 'external' 
files are formatted correctly.) 

I've tried to follow these instructions from http://www.odose.nl/ (Analyze Data 
tab) - 

>"User-generated whole-genome data not yet archived in GenBank can be uploaded 
>to be analysed separately or in conjunction with published genomes. To do 
>this, first create a new history: in the right ‘History’ pane go to Options > 
>Create New. In the left ‘Tools’ pane go to Get Data > Upload File and select 
>one or multiple .ffn files from your computer and click ‘Execute’..."

This worked fine.

>"Go to Divergence > Upload genomes in the ‘Tools’ pane, press the ‘Add new 
>genome’ button, specify a genome label and press ‘Execute’ for each genome to 
>be included…"

I was unable to find a "Divergence" option in the Tools pane.  So, I assumed 
this should be O'DoSE > Upload Genomes, in the Tools Pane.  Using this 
function, I uploaded each genome and selected "Execute." 

>"Proceed to the Workflow menu to add listed genomes and/or to specify input 
>settings…"

Perhaps this is my downfall, but I was unable to see how to add genomes in the 
Workflow menu. 

At this point, I had uploaded four genomes, and attempted to select the first 
option in the analysis: "Extract & Translate Genes."  I chose the option of 
selecting my external genomes, but the analysis failed, giving the error 
"History does not include a dataset of the required format/build" error.  This 
error appears within the "Genbank Project ID's" box.  In this case, I have no 
Genbank Project ID's, because all data are external genomes.

Interestingly: 

The problem is solved by selecting at least one genome from the Complete 
Microbial Genomes table.  Selecting one genome generates a Project ID list.  I 
am then able to perform "Extract & Translate Genes" and all further functions, 
acting on the set of external genomes and the one selected (internal) genome.   
I've tried this several times, with different external genome files.  I can 
successfully analyze dozens of external genomes, but _only if_ at least one 
'internal' genome is selected as well. 


I need to run an analysis on a set of genomes that is exclusively unpublished, 
so the data will be entirely "external" genomes. Including a published genome 
will throw off the comparisons we need to make.

Based on the ODoSE instructions above (that user-generated whole-genome 
data...can be uploaded to be analysed separately or in conjunction with 
published genomes), I sense I should be able to use exclusively 'external' 
genomes in an analysis.  Do you have any suggestions on how I can do this?   
Any advice would be much appreciated. 

thank you, 
Jen

(Apologies to the moderator for the earlier version of this message that was 
too large.  Above, I've removed the attachments showing screen shots.  I hope 
the problem is clear from the History link above.)


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