Question: Can i upload file with extension gz?
gravatar for lnaren
3.1 years ago by
lnaren10 wrote:


Can I upload a 17G DNA sequence data file with extension .fastq.gz through FTP?



ftp • 912 views
ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson25k • written 3.1 years ago by lnaren10

As long as it's within the quota (250 GB on the public instance), it should be fine.

ADD REPLYlink written 3.1 years ago by vladimir.gritsenko90

I haven't use any of the quota yet, my history is empty.But I couldn't upload this .gz file using FTP. Is it because the file is compressed?

ADD REPLYlink written 3.1 years ago by lnaren10

I think Galaxy should handle that compression. What error are you getting?

ADD REPLYlink written 3.1 years ago by vladimir.gritsenko90
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Data in filename.gz format can be loaded via FTP (See Support#Loading_data). The data will be uncompressed during upload and must be under 50 GB in size (the individual upload file size quota).

If your data is over 50 GB uncompressed, loading portions of it then merging once in Galaxy can be an option. See this prior post for pro/cons of this method: Illumina DNA sequence upload problem

Data with a name like filename.tar.gz may or may not load. Tar archives are not a supported compression format. If such an archive does happen to upload (some will), only the first file in the archive will be extracted by Galaxy. This is generally undesirable. Instead, extract the contents of the archive locally, then upload to Galaxy the individual files you want to work with.

If your data is in filename.gz format, known to be under 50 GB in size uncompressed, and still fails upload - there are a few options for troubleshooting/workarounds:

  1. Uncompress the file and load it that way. Not all "gz" compressed data uses a consistent archive procedure. This method removes compression variances as a load factor, with the bonus of alerting you to problems with the compressed file itself (it if fails to uncompress locally, then it will probably fail in Galaxy).
  2. Strongly consider using an FTP client such as FileZilla to manage the load. Resuming interrupted transfers and tracking full load success are just some of the advantages. If one is not comfortable on the command-line, an FTP client aids with accessibility as well.

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k
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