Question: Problems transferring FASTQ file from EBI to galaxy
gravatar for ang3x
23 months ago by
ang3x20 wrote:

I have never had problems transferring FASTQ files from EBI to my galaxy site. Beginning last week, I have been unable to transfer SRR772111. I have successfully transferred this in the past. I get inconsistent error messages including site unavailable and trouble with decompressing, and sometimes the transfer just runs without completing.

chip-seq • 700 views
ADD COMMENTlink modified 23 months ago by scholtz60 • written 23 months ago by ang3x20
gravatar for scholtz
23 months ago by
scholtz60 wrote:


This is the reponse I received from the EBI folks to my inquiry - the problem will hopefully be resolved by next week :))



"On 2017.01.06., at 13:50, Marc Rossello wrote:

Dear colleagues,

The problems with the FTP servers that were limiting data downloads (or transferring files to Galaxy) have now largely been resolved and connections can be made and data downloaded. We are expecting the service to be stable by EOB today. It is still in an "at-risk" condition and the performance could be slower than usual until the beginning of next week.

Sorry for the inconvenience.

Regards, Marc"

ADD COMMENTlink written 23 months ago by scholtz60
gravatar for Mo Heydarian
23 months ago by
Mo Heydarian830
United States
Mo Heydarian830 wrote:


There are currently issues with data retrieval from EBI SRA, their technical team is working on fixing it.

In the meantime, you can use NCBI SRA Tools for SRA data retrieval. See this post about importing paired end data with NCBI SRA Tools.

Hope this helps!


Mo Heydarian

ADD COMMENTlink written 23 months ago by Mo Heydarian830
gravatar for radhika.patel
23 months ago by
United Kingdom
radhika.patel0 wrote:

Been having the same problem for a few weeks. I tried the SRA Tools but the workflows consistently resulted in errors when I tried this. Have resorted to downloading the files to my computer and then uploading them to Galaxy via an FTP server. Does anyone have a better solution?

Thanks, Radhika

ADD COMMENTlink written 23 months ago by radhika.patel0

Can you share the issues you are having with switching to NCBI SRA Tools with your analysis?

You may have noticed, but if you use NCBI SRA Tools with single entries to retrieve paired end data, both the forward and reverse reads are dumped to the same file. See here for how to import paired end data as split (forward/reverse) files.

Cheers, Mo Heydarian

ADD REPLYlink written 23 months ago by Mo Heydarian830
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour