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. -Dannon On Nov 13, 2012, at 9:19 AM, rolandomantilla1@gmail.com wrote:
Sent from my Verizon Wireless BlackBerry From: Rolando Mantilla <rolandomantilla1@gmail.com> Date: Mon, 12 Nov 2012 19:31:20 -0800 To: <galaxy-user@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 reads. 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. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: