SRR dataset not available: Connection drops from NCBI using fastq_dump -- try Upload by URL instead

Hi! I am new to Galaxy. I am trying to Download and Extract Reads in FASTA/Q** format from NCBI SRA of an accession number SRR643156. But the job submission fails. It says “The server could not complete this request. Please verify your parameter settings, retry submission and contact the Galaxy Team if this error persists. A transcript of the submitted data is shown below.”

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Hi @natkochanova

Sometimes NCBI gets busy, and sometimes the connection between Galaxy and NCBI drops. The solution is to try again.

To eliminate technical issues – reload the tool form from the right tool panel (will be the most current version), make sure that you just type in the accession (not other content or characters, including avoiding whitespace), then submit.

Try at least twice more as needed. You can start those up concurrently. If both work, purge the extra dataset to recover quota space. If both fail, then you can capture the data’s URL directly from NCBI and paste it into the Upload tool and load it that way. That method uses a different connection method and is a good solution to try whenever NCBI is busy/problematic when using the fastq_dump method.

Find your particular accession here: Run Browser : Browse : Sequence Read Archive : NCBI/NLM/NIH

Hope one of those work out!

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