GSE accession upload creates grey datasets with 0 pairs on usegalaxy.org

[prabalraj]

I am using usegalaxy.org and tried to import data using a GSE accession with the SRA/ENA download tool.

The job completed, and I received:

• One paired-end dataset (green) with 6 fastqsanger.gz pairs

• One single-end dataset (green)

• Two additional outputs that are grey:

  • “Paired-end data (fastq-dump)” – a list with 0 pairs

  • “Single-end data (fastq-dump)” – a list with 0 datasets

The grey datasets show no errors, just empty collections.

Is this expected behavior when the GSE contains only certain library types?
Or does this indicate a problem with how Galaxy classifies the runs?

Server: usegalaxy.org
Tool used: SRA/ENA download via GSE accession

[jennaj]

Welcome @prabalraj

The first set of outputs looks correct! The data are sorted into the collection type they belong to. It seems you had 6 SRA accessions corresponding to paired end reads at ENA. The output is similar to the output from the NCBI SRA tool and how to process the reads will be similar.

Then, the second set of outputs might be correct – or it might be a duplicate from clicking on a button twice. This appears to be a second run of the same tool or did you really have two distinct queries, both with 6 accessions?

For the jobs queuing part, this is normal and expected! See queued-gray-datasets for prior discussion. But if this was just a double click, you can delete those duplicated queued jobs to stop them from executing and loading more data into your history.

A double submit click is likely what happened, but if you think more is going on, would you like to explain what you are doing (screenshots may help) and we can try to help optimise your protocol?

Please let us know!