Failed Uploads from EBI SRA to import to Galaxy

Question: Failed Uploads from EBI SRA to import to Galaxy

23 months ago by

I am unable to load anything from EBI SRA. I have not been able to for a few days. It starts, and then it turns red. Is this a known issue? I have bug reported several times already.

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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 23 months ago by biologistcandiceyoung • 30

Hello, I am also seeing failed uploads from EBI SRA. A temporary solution is to use "NCBI SRA Tools -> Extract reads in FASTQ/A format from NCBI SRA".

A sidenote: if you're using a custom Galaxy instance, be sure to update SRA tools to version 2.8.0 (earlier versions are not compatible with the recent NCBI updates). UseGalaxy.org has SRA tools version 2.8.0 available.

Thanks for using Galaxy!

Cheers, Mo Heydarian

ADD REPLY • link written 23 months ago by Mo Heydarian ♦ 830

I appreciate your suggestion, but I am still seeing the same situation occur with that method as well...

ADD REPLY • link written 23 months ago by biologistcandiceyoung • 30

Hello, Which Galaxy instance are you using? What error message do you see and do you see it for all datasets you try to import?

This information may help reveal the issue and hopefully find a workaround in the meantime.

Cheers, Mo Heydarian

ADD REPLY • link written 23 months ago by Mo Heydarian ♦ 830

23 months ago by

Mo Heydarian ♦ 830

United States

Mo Heydarian ♦ 830 wrote:

Hello,

Can you share the first hundred lines of the FastQ files you retrieve from EBA SRA and NCBI SRA? Alternatively, you can check yourself to ensure the reads are formatted the same way. One known issue with the NCBI SRA Tools wrapper is that it imports paired end data as one FastQ file. This could skew your analysis if the paired reads are not split.

Cheers, Mo Heydarian

ADD COMMENT • link written 23 months ago by Mo Heydarian ♦ 830

23 months ago by

biologistcandiceyoung • 30

biologistcandiceyoung • 30 wrote:

I apologize for being so persistent with this, but there is still an issue with the uploads. The extract files tools allows me to upload samples however, when I test those against the samples already run, they yield completely different results. For instance, where I would use Bowtie and get 1.58% (Get Data>uploads from EBI SRA sequences) alignment, I would get 0.00% alignment (NCBI SRA tools> Extract files). This is a HUGE margin given the nature of my research.

ADD COMMENT • link written 23 months ago by biologistcandiceyoung • 30

23 months ago by

biologistcandiceyoung • 30

biologistcandiceyoung • 30 wrote:

I am using the main galaxy at usegalaxy.org. All imports fail to upload.

Unable to fetch ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR102/008/SRR1027188/SRR1027188_1.fastq.gz: [Errno 104] Connection reset by peer

Fatal error: Exit code 2 () /galaxy-repl/main/jobdir/014/658/14658998/tool_script.sh: line 9: [: SRR1027188: unary operator expected

Above are the error codes I continue to receive. The top error message from Get Data, EBI SRA the second from EBI SRA Extract.

I'm so disappointed that I haven't been able to run any samples for several days now.

Please fix as soon as possible.

Much appreciated.

ADD COMMENT • link written 23 months ago by biologistcandiceyoung • 30

Hello, Thanks for the additional information.

I just tried importing SRR1027188 with "NCBI SRA Tools -> Extract reads in FASTQ/A format from NCBI SRA" using the default options and was able to successfully import the SRR1027188 fastq file. Can you try again on your end?

Cheers, Mo Heydarian

ADD REPLY • link written 23 months ago by Mo Heydarian ♦ 830

23 months ago by

biologistcandiceyoung • 30

biologistcandiceyoung • 30 wrote:

Same result. Failed. I would like to send a screenshot... Please inform.

ADD COMMENT • link written 23 months ago by biologistcandiceyoung • 30

Sorry to hear. You can send the screenshot to mo_at_galaxyproject_dot_org. You can also share a history with examples of failed attempts to import your data with the same email address/username on usegalaxy.org (this will be informative).

Cheers, Mo Heydarian

ADD REPLY • link written 23 months ago by Mo Heydarian ♦ 830

22 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Issue with the tool Get Data > EBI SRA are undergoing resolution. Details here: https://biostar.usegalaxy.org/p/21066/

Thanks for reporting the problem, Jen, Galaxy team

ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k

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