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Question: Galaxy: uncompleted uploading files from URL show up in green
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gravatar for n.goue
20 months ago by
n.goue • 50
n.goue • 50 wrote:

Hi, I tried to import fastq.gz files from URL to our galaxy instance (v17). Some files seems to be downloaded completely (4 to 5 Gb), other don't (< the expected size). All of them appear in green box in the history. If I try and continue working with the looks-like complete file, doing a FASTQ Groomer for example I got an error message : "gzip: /data/galaxy/galaxy-server/database/files/000/dataset_381.dat: unexpected end of file". The files definitely didn't upload correctly despite the green box and I have no error message in the log file. Is there some settings I should modify in the Galaxy configuration files? Could someone help me ? Thanks!
rna-seq import file galaxy • 536 views
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modified 20 months ago • written 20 months ago by n.goue • 50
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gravatar for Jennifer Hillman Jackson
20 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If the file is not served from the remote server completely, this can occur. Galaxy has no way of knowing if loaded data is complete or not. Any data uploaded should be double-checked for completeness no matter what the source/upload method.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 20 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for n.goue
20 months ago by
n.goue • 50
n.goue • 50 wrote:

Hi,

What do you mean by if file is not served completely ?

If its about the md5sum, I checked it after I copied the files to the server.

Thanks,
ADD COMMENT • link written 20 months ago by n.goue • 50
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