I am very new to galaxy and it is my first problem I have gz archive with .fastq, but when it unpacking it still .fastq (not .fastq.gz) And when I upload my file it appears to the right and it is red. Galaxy writes “file not found” or next error:
Internal Server Error
Galaxy was unable to successfully complete your request
An error occurred.
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
I suppose I need only format .fastq.gz but how create it?
Any help would be appreciated
The extension of the file is one of these, correct?
.fastq .fastq.gz .fastqsanger .fastqsanger.gz
Galaxy should be able to autodetect the datatype for these read files when using the Upload tool.
This should be temporary for anyone.
I am running a test at UseGalaxy.org to double check that there is not a problem server side. More feedback soon. The tests for using the Upload tool for local file browsing, pasted URL, and fetching reads from NCBI were all successful.
Some of these test jobs did queue first, indicating that the server is very busy.
If you are loading data from your computer (local file browsing), make sure to stay logged into Galaxy until the process fully completes or the job will error similar to your reported issue.
If you are loading data with public URLs, or via tools that directly fetch reads from data providers (NCBI or others), this will not require you to stay logged into Galaxy. Just make sure the job is fully started and output datasets appear in the History (queued, executing, or completed).
Exception: there are rare circumstances when the specific compression program used to generate the gz format is not understood by Galaxy. The solution is to try to load uncompressed reads instead. You can then re-compress the reads in Galaxy or use them uncompressed.
These two tutorials cover general information about how fastq read data is handled and labeled in Galaxy. That training site can also be searched or navigated to find analysis domain protocols with more examples of read data plus workflows.