Imported file size

usegalaxy.eu support
1

Hi,

I am trying to import 3-5GB fastq.gz MG files into Galaxy, and the imported file sizes are smaller than the original ones. What should I do to fully import my files?

Thanks!

2

Hi @earthworm

If you really think that the connection between your computer and the Galaxy server is dropping out, the process will usually end in an error – in the Upload tool itself or as a “red” dataset in the history. This would be especially true for a compressed file. So, maybe something else is going on.

You could run this command on your data locally and one in Galaxy to compare → Secure Hash / Message Digest. The md5 option is usually a good choice. If you are not sure how to run that on your computer – try an internet search, since the exact command can differ by operating system.

Other items:

  1. It is important to not navigate away from the Upload view while loading data. Closing the pop-up window is Ok, but moving to some of the other views is not. So, try waiting first if it seems that is going on.
  2. Let Galaxy auto-detect the datatype for any fastq data. This avoids other types of potential conflicts … beyond just file sizes.
  3. Loading uncompressed data is sometimes needed. Some small fraction of local compression file types might be not understood, and this gets around that problem. You can always re-compress once in Galaxy.

Two other solutions when working at the UseGalaxy.eu server.

  1. Use the resume function in the Upload tool. This only shows up as an option when an interrupted connection is still available … and might not be your use case if the data does load successfully (results in a new “green” dataset in the history) but the size just seems off.
  2. The EU server hosts an FTP function. The URL of where you are working is important for a successful connection to the right server. Can be a choice for batches of data but usually not needed for one or a few files anymore since the resume function handles those fine. Upload many files (>10) via FTP

Give that a review, then maybe share more details if things are still going wrong. Screenshots would probably help to clarify more for this.

3

Thanks. Uploading the files on FTP server went well. However, the file size dropped again when I imported files to Galaxy from the FTP directory. Could there be any way to address this problem?

4

Continued at File import size issues