Question: Galaxy: uncompleted uploading files from URL show up in green
0
gravatar for n.goue
10 months ago by
n.goue30
n.goue30 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 • 301 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by n.goue30
0
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 10 months ago by Jennifer Hillman Jackson23k
0
gravatar for n.goue
10 months ago by
n.goue30
n.goue30 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 COMMENTlink written 10 months ago by n.goue30
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