I used a single end fastqsanger file ( related to the leaf of Solanum ) and tried to run trinity to get assembled transcript data, but after the program was run, i got 0 bytes generated and no transcript.fasta file was generated. why ?
I found the issue. It has to do with a current problem with the Get Data > EBI SRA tool. Details here: https://github.com/galaxyproject/galaxy/issues/6334
In short, reassign the datatype to be "fastqsanger.gz" for your fastq inputs. The data is compressed but is not being labeled that way -- we'll be fixing that. Follow the ticket above for updates.
How to change metadata is in the Galaxy FAQs: https://galaxyproject.org/support/
- How do I find, adjust, and/or correct metadata? https://galaxyproject.org/support/metadata/
I would still recommend doing some QA on the data before attempting assembly or the tool may really run out of memory during job execution due to content issues.
And single-end Trinity jobs are confirmed to be functional at this server.
Thanks! Jen, Galaxy team
So we can change the type by going to edit attributes right? So first get the data from ENA and then change its type to fastqsanger.gz and then run the trinity . Right?
Yes, until the tool is fixed that will need to be done.
Or, if your accession is at NCBI, the tool NCBI SRA Tools > Download and Extract Reads in FASTA/Q format from NCBI SRA can be used instead. That tool sets the metadata correctly depending on the output datatype selected on the form.
Single end input should be possible. I am running a quick test to make sure that functionality is intact at Galaxy Main.
Could you confirm that you are working at Galaxy Main https://usegalaxy.org? If not, where are you using Galaxy?
Ok, I found your jobs. This might be a memory failure but will confirm that. Meanwhile, you might want to do some QA on the reads before assembly. Please do not delete the failed job(s) quite yet - they do not consume any quota space.
Galaxy tutorials, including those that cover QA/QC: https://galaxyproject.org/learn
Thanks and more feedback soon, Jen, Galaxy team