Download and Extract Reads in FASTQ: Troubleshooting Fatal error: Exit code 2 ()

[abhi_g]

I have also faced the sample problem when extracting an sra file using Download and Extract Reads in FASTQ tool. Kindly share your help.

[jennaj]

Welcome @abhi_g

Hopefully you have tried to load the data again to eliminate transient connection problems! If not, please try that first. SRA can get busy sometimes and drop connections to anyone making a query (including from Galaxy).

Should that not be enough, you are welcome to share back your job for some feedback. Maybe something small needs to be adjusted. The tool you reference is intended to retrieve fastq sequence reads. Other types of SRA data will use different tools.

Screenshots may be enough, or you can share your history and we’ll be able to see all the details that way. This would also allow us to see if SRA itself has some problem with the specific query. See → How to get faster help with your question

Hope this helps! Please let us know how this turns out.

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Xref

Example for a batch retrieval. → Hands-on: From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis / Variant Analysis

Retrieval and QA. → Quality Control Start Here! multQC issue and guidance?

@jennaj

Q&A

I tried to retrieve a batch of accessions from NCBI SRA, but the query failed!

First, check your query terms. Most of these underlying tools expect one accession term per line without any extra spaces or blank lines. You can confirm by reviewing the tool form instructions.

Next, try again! External data services can get busy and reject queries for unclear reasons. Trying again at a different time is a common solution.