CAMERA Blast output - invalid XML?

[MikeT]

Hi all,
I've ran some of my datasets on the tBLASTx program on the CAMERA portal. Since the hit number was quite big, the portal let me download the output as a .xml file.
Sadly, as I run blast_formatter on the .xml it appears to be an invalid file format: Galaxy tells me it's a simple .txt, instead of a .xml. How can I reformat it?

-MikeT

[maubp]

Can you show us the first 10 lines or so using the [ code ] and [ /code ] forum tags to preserve the formatting? Try using the Unix command 'head' for this,

head -n 10 example.xml

[MikeT]

Here's a screenshot of the first lines:

http://www.box.com/s/d9b5d73367bdb67e3617

Hope it helps!

-MikeT

[maubp]

Here's a screenshot of the first lines:

http://www.box.com/s/d9b5d73367bdb67e3617

Hope it helps!

That does look like BLAST XML.

It is possible Galaxy failed to auto-detect the file type. You can set this explicitly when you upload a file to Galaxy. Or, after uploading from the history entry use the "pencil" icon ("edit attributes") to change the filetype.

Sadly, as I run blast_formatter on the .xml it appears to be an invalid file format

The NCBI tool blast_formatter does not expect an XML input, rather an ASN.1 file.

[MikeT]

That does look like BLAST XML.

It is possible Galaxy failed to auto-detect the file type. You can set this explicitly when you upload a file to Galaxy. Or, after uploading from the history entry use the "pencil" icon ("edit attributes") to change the filetype.

Already tried, but when I do it and then use the "Parse BLAST output" command it still doesn't recognize the file as a .xml BLAST output.

The NCBI tool blast_formatter does not expect an XML input, rather an ASN.1 file.

Are you sure? Because the -help section for the tool explicitly says that it expects some ASN.1 files and .XMLs. Anyway, how can I reformat my output as an ASN.1 file?

-MikeT

[maubp]

Already tried, but when I do it and then use the "Parse BLAST output" command it still doesn't recognize the file as a .xml BLAST output.

In that case (assuming you are using the public Galaxy), write to the galaxy-users mailing list and offer to share a history with the problematic XML file with them for diagnosis.

Are you sure? Because the -help section for the tool explicitly says that it expects some ASN.1 files and .XMLs. Anyway, how can I reformat my output as an ASN.1 file?

I only have BLAST 2.2.25+ installed on this machine (the latest is now 2.2.26), and it doesn't say that in the 'blast_formatter -help' text. I doesn't say much at all about the -archive argument, but the website is pretty clear it expects a BLAST archive format (ASN.1) file: http://www.ncbi.nlm.nih.gov/books/NBK1763/