It looks like you have conflicting blastxml entries. Edit your
datatypes_conf.xml to remove any references to blastxml (the toolshed manages
datatypes separately), restart galaxy, and you should be good to go.
On Nov 13, 2012, at 9:19 AM, rolandomantil...@gmail.com wrote:
> Sent from my Verizon Wireless BlackBerry
> From: Rolando Mantilla <rolandomantil...@gmail.com>
> Date: Mon, 12 Nov 2012 19:31:20 -0800
> To: <galaxy-u...@lists.bx.psu.edu>
> Subject: Warning message
> I'm having issues with the FASTQ_Groomer. What I have done it first I
> downloaded an SRA file created by an Ion torrent sequencer from the NCBI
> site. Then used the fastq-dump app from the NCBI site to covert the .sra file
> to .fastq file. When I uploaded the data into galaxy it recognized it as a
> fastq(as it should) but when I try to run the FASTQ groomer I get the message
> and warnings below. I also have already downloaded the the blast_datatypes
> tool from the tool_shed. I truly don't know what the issue is, any help
> An error occurred running this job: Groomed 12376 sanger reads into sanger
> WARNING:galaxy.datatypes.registry:Error loading datatype with extension
> 'blastxml': 'module' object has no attribute 'BlastXml'
> WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with
> extension 'blastxml', using datatype from /mnt/galaxyData/tmp/tmpdP_cZ7.
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