Question: generating 0 bytes for trinity assembled transcript file
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gravatar for manjumoorthy95
4 weeks ago by
manjumoorthy950 wrote:

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 ?

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by manjumoorthy950

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?

ADD REPLYlink written 4 weeks ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Jennifer Hillman Jackson25k
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gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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/

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

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Jennifer Hillman Jackson25k
0
gravatar for manjumoorthy95
4 weeks ago by
manjumoorthy950 wrote:

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?

ADD COMMENTlink written 4 weeks ago by manjumoorthy950

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.

ADD REPLYlink written 4 weeks ago by Jennifer Hillman Jackson25k
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