Welcome @David_R
The memory not being specified in the string is Ok, it just means it will be set by the cluster environment instead (at a higher level).
Instead, the tools seems to be having trouble reading in the input file. Let’s go through the details and come up with next steps!
Screenshot
Tool form → RepeatExplorer (clustering) repeat discovery and characterization using graph-based sequence clustering(Galaxy Version 2.3.8+galaxy0) as hosted at UseGalaxy public servers
Expected inputs
- Dataset with the
fastadatatype format assigned- “Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended.”
- Choice made to specify whether the reads are single or paired end
- “If paired-end reads are used, they must be interleaved and all pairs must be complete.”
How did your dataset and the options set compare to this? You can post screenshots or share your history back here if you would like help. → How to get faster help with your question
You can also do some checks yourself.
If the file is in fasta.gz format, the datatype fastagz will be assigned by the Upload tool. Then, when this tool is executed, there will be a automatic file format conversion process to uncompress the data at runtime. The uncompressed version of the data will be in your history. If this process had some problem, it usually means that something went wrong with the assigned datatype format (a mismatched label for the actual content) or that the file is compressed on a way that Galaxy cannot interpret.
However – since you used FTP I’m also curious about which server you were working at and how that was done. This was at UseGalaxy.eu, correct? Maybe there is some problem.
What to try
- Start here → Run the tool FastqInfo on the file to check the formatting/compression.
- Verify the single/paired content inside the file and make sure the toggle on the form is the same. Interleave the data first if needed.
- Consider uncompressing the file yourself first (pencil icon - Edit attributes) then submitting the
fastaversion instead to see what happens. - Possibly Upload the file again and make sure to use the autodetect option to allow Galaxy to guess the datatype. → Getting Data into Galaxy.
- In rare cases, loading up the uncompressed version of a file is needed. There are a few versions of
gzout in the wild that are not compatible.
If the input and options all check out, and a rerun still fails, then the problem could be on the server itself, maybe an issue with the tool wrapper. We can help to confirm and alert the administrators if you share your history example or even just the server URL and exact tool version so we can try to reproduce the issue. Maybe FTP at the EU server has some issue but if you are working somewhere else, that would be important to know.
So – I’ll test FTP at EU and you can do a few checks on the file itself. If it didn’t load into the history, other tools will fail too – so, starting with the Fastq Info tool will reveal that.
Hope this helps and we can follow up more! . 