Question: Metadata galaxy error
0
gravatar for VY
3.2 years ago by
VY120
London
VY120 wrote:

Is there an issue with galaxy? I've uploaded .bam files that were aligned against mouse mm9 and a flag keeps coming up that galaxy has encountered an error setting the metadata, and when I do it manually the same flag keeps coming up. Also it won't allow me to do any downstream analysis such as MACS peak calling, an error = invalid block length.

 

Any suggestions, or is this a bug?


Thanks

metadata galaxy • 1.1k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by VY120
0
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

There are no known issues on the public Main Galaxy instance at http://usegalaxy.org. If using Main, then there is either a file upload issue (make sure to use FTP) or a format issue in the original data. If using a different server, contact the administrator hosting the instance.

Best, Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k

The issue i'm having and can't seem to resolve is that I am uploading my aligned bam files via FTP onto the public main galaxy instance. The only thing i've done is select from the dropdown that the alignment was done against mouse mm9. Once the files are in my history a yellow flag appears saying that "an error occurred setting the metadata for this dataset" which I tried to resolve by going to the attributes and setting the datatype to bam but that does not resolve it either. This prevents me from doing anything else downstream with the bam files and thats what made me ask if there is possible an issue with the server. 

 

Also when I do set the database/build to mm9 the flag disappears but again I can not do anything with the file. If I try to view it in IGB or IGV a message comes up saying " There was a conflict when trying to complete your request. 
Error generating display_link: type object 'Bam' has no attribute 'name' " 

Any suggestions you might have would be greatly appreciated.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by VY120

Hello, Were you able to manipulate the BAM file locally? BAM files can also be viewed locally in IGV - how does that work? The reason why I am asking is that it sounds very much as if there is a problem with the source BAM files themselves, not Galaxy or the upload function. Please let us know. Thanks, Jen, Galaxy team

ADD REPLYlink written 3.2 years ago by Jennifer Hillman Jackson25k

Hello Jen and thank you for your help, IGV could not open the files locally either so I deleted them and re-downloaded them from the database manually. Apparently downloading via FTP programs (such as Cyberduck) can corrupt big files such as .bam. It's all sorted now. 

 

Thanks for all the input

ADD REPLYlink written 3.2 years ago by VY120

Glad to know all is working and we appreciate the feedback! Jen

ADD REPLYlink written 3.2 years ago by Jennifer Hillman Jackson25k
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