Question: Uploading data to galaxy
gravatar for stafford.vigors
17 days ago by
stafford.vigors0 wrote:

I am having an issue uploading files onto the galaxy server. It comes with an error, problem decompressing gzipped data. Can you help with this issue?

rna-seq • 61 views
ADD COMMENTlink modified 16 days ago • written 17 days ago by stafford.vigors0
gravatar for Jennifer Hillman Jackson
17 days ago by
United States
Jennifer Hillman Jackson21k wrote:


Some reports of upload failures have come in. These are no longer reproducible and the root cause is not known. The first pass solution is to try it now, then troubleshoot if you are still having problems.


  • When .gz compressed data fails to uncompress the issue is usually an incompatibility between the server resources used to uncompress data and the compression resources used to create the file. That or the file is over 2 GB and was browsed for upload instead of FTP being used.

  • If the failure is persistent even with FTP, then uncompress the data before loading into Galaxy. This also helps find problems - if the data will not uncompress locally, it will not uncompress in Galaxy, generally indicating that the file is not complete due to an earlier partial transfer upstream of Galaxy.

Help for upload:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 17 days ago by Jennifer Hillman Jackson21k


Has the "leave .gz files compressed" function/policy been disabled? I have just uploaded a batch of gzip files and they were automatically decompressed to my surprise.


ADD REPLYlink written 17 days ago by Bao Ho50

Assign the datatype fastq.gz or fastqsanger.gz to the file in the upload tool. This will preserve the compressed format.

If datatype autodetect (default) is used then the file will uncompress.

ADD REPLYlink written 17 days ago by Jennifer Hillman Jackson21k
gravatar for stafford.vigors
16 days ago by
stafford.vigors0 wrote:

Hi thank you for your advice, I tried some of the advice and it seems that my files may be too big to upload, I have also tried uploading using filezilla ans also importing directly from NGS provider. When I try to import directly from the provider site I get this message ,urlopen error ftp error: 503 Login with USER first' I think if I can get this working this may be the best option, any advice?

ADD COMMENTlink written 16 days ago by stafford.vigors0
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