Question: Failed Uploads from EBI SRA to import to Galaxy
2
gravatar for biologistcandiceyoung
23 months ago by
biologistcandiceyoung30 wrote:

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.

software error galaxy • 1.2k views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 23 months ago by biologistcandiceyoung30
1

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 REPLYlink written 23 months ago by Mo Heydarian830

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

ADD REPLYlink written 23 months ago by biologistcandiceyoung30
1

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 REPLYlink written 23 months ago by Mo Heydarian830
2
gravatar for Mo Heydarian
23 months ago by
Mo Heydarian830
United States
Mo Heydarian830 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 COMMENTlink written 23 months ago by Mo Heydarian830
1
gravatar for biologistcandiceyoung
23 months ago by
biologistcandiceyoung30 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 COMMENTlink written 23 months ago by biologistcandiceyoung30
0
gravatar for biologistcandiceyoung
23 months ago by
biologistcandiceyoung30 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 COMMENTlink written 23 months ago by biologistcandiceyoung30
1

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 REPLYlink written 23 months ago by Mo Heydarian830
0
gravatar for biologistcandiceyoung
23 months ago by
biologistcandiceyoung30 wrote:

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

ADD COMMENTlink written 23 months ago by biologistcandiceyoung30

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 REPLYlink written 23 months ago by Mo Heydarian830
0
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 22 months ago by Jennifer Hillman Jackson25k
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