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Question: galaxy doesn't recognise dbSNP file I uploaded
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gravatar for henryrobins3
3.2 years ago by
henryrobins3 • 0
European Union
henryrobins3 • 0 wrote:

Hi

I'm somewhat new to the game and struggling with the GATK unified genotyper.

I found a dbsnp file (in vcf format) but Galaxy isn't recognising it as a vcf file. I tried modifying it under attributes and that changed the file type to vcf but galaxy still isn't accepting that I have a vcf file.

I then noticed there was a message on the file itself saying that galaxy had a problem uncompressing the zipped data, so i've unzipped and am uploading again but the file is 27gb and i'm running out of space! All of my fastq files were zipped and that wasn't a problem.

Surely there is an easier way? Any thoughts would be much appreciated.

Cheers 

Henry
gatk • 853 views
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modified 3.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.2 years ago by henryrobins3 • 0
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gravatar for Jennifer Hillman Jackson
3.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Any dataset is unzipped/uncompressed once loaded into Galaxy upon upload anyway, so loading it uncompressed just takes upload time. The size in a history will remain constant. If it uncompresses locally, but not in Galaxy for some reason, then load it uncompressed. Use a client such as FileZilla to manage the FTP (if needed) and resume transfer if it is interrupted, until the entire dataset is loaded. Do watch the disk space usage - if it goes over the 250 GB quota, then no work can be done until this is reduced.

If more resources are needed for the work, then a Cloud Galaxy could be a solution. AWS offers educational/research grants to help with costs. Galaxy Choices: https://wiki.galaxyproject.org/BigPicture/Choices

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k
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