Question: Warning Message
gravatar for Rolando Mantilla
6.0 years ago by
Rolando Mantilla10 wrote:
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.
galaxy • 911 views
ADD COMMENTlink modified 6.0 years ago by Daniel Blankenberg ♦♦ 1.7k • written 6.0 years ago by Rolando Mantilla10
gravatar for Daniel Blankenberg
6.0 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:
Hi Rolando, You'll need to remove the old blast datatypes from your datatypes_conf.xml file. If you haven't added any new datatypes manually yourself, you can copy the datatypes_conf.xml.sample file over of your datatypes_conf.xml file. Also, in the future questions about local Galaxy instances should be sent to the galaxy-dev mailing list. Thanks for using Galaxy, Dan
ADD COMMENTlink written 6.0 years ago by Daniel Blankenberg ♦♦ 1.7k
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