Failed to download data from EBI BioStudies with ascp/Aspera

Question

[biock]

Hello,

I am trying to download data from EBI's ENA database through ascp (version 4.3.0.93, aspera version: 4.1.3.93):

ascp -P33001 -i "asperaweb_id_dsa.openssh" [e-mail]:/S-BSST/012/S-BSST12/Files/aeipf_denoised_reads.fna ./

But I met the following error:

Session Stop  (Error: Server aborted session: Authorization refused: user/group bsaspera denied by server.  Auth value is token)

Does anyone know why this error happens? Thanks!

[GenoMax]

Hopefully it is a temp issue on ENA end. If you continue to have problems email their help desk.

[孝中]

Hi, have you found the solution to this problem?

[jude]

I'm also facing the same error

[ruiyan_hou]

I also face this problem. Have you fixed this problem?

Thanks !

[Michael]

We have been facing the same problem. I will look into it.

[ruiyan_hou]

Could anyone who fix this question tell us how to fix it?

Thank you!

[ATpoint]

Please email EBI and dont post duplicates. Especially not as an answer.

[Michael]

Please check my answer. No need to send an email to EBI either.

Answer 1

[Michael]

Anonymous Aspera download from ENA works as expected.

Please follow the official documentation https://ena-docs.readthedocs.io/en/latest/retrieval/file-download.html

You might have been confused by some outdated documentation at https://www.ebi.ac.uk/biostudies/help#

The correct hostname to download data is as follows:

ascp -P33001 -i <path to asperaweb_id_dsa.openssh> [e-mail]:vol1/fastq/ERR164/ERR164407/ERR164407.fastq.gz ./

ERR164407.fastq.gz                            100%   72MB  342Mb/s    00:02
Completed: 74523K bytes transferred in 2 seconds
(247650K bits/sec), in 1 file.

asperaweb_id_dsa.openssh comes with the ascp client. I have sent a request to EBI to remove or update the outdated documentation.

This answer was provided by me on behalf of Elixir Norway. If you find this post helpful, please upvote/accept the answer.

[ruiyan_hou]

Hi Michael, I still cannot download.

Actually I want to download E-MTAB-6798 from ENA. https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6798

I click the download for processed data and then it will appear a new chatbox. Next I download E-MTAB-6798-unix-aspera.sh which includes command.

ascp -P33001 -i "C:/aspera/cli/etc/asperaweb_id_dsa.openssh" --host=fasp.ebi.ac.uk --user=bsaspera --mode=recv  "fire/E-MTAB-/798/E-MTAB-6798/Files/3040sTS.Mouse.Brain.12.5.Male.sorted.bam" ./

It will give me the error :

Session Stop  (Error: Server aborted session: Authorization refused: user/group bsaspera denied by server.  Auth value is token)

But If I changed the host and user according to your answer, it will send another error.

(Py39) [ruiyanhou@CPU3:Chicken]$ ascp -P33001 -i "/mnt/ruiyanhou/nfs_share2/conda_env/envs/Py39/etc/asperaweb_id_dsa.openssh" --host=fasp.sra.ebi.ac.uk  --user=era-fasp --mode=recv  "fire/E-MTAB-/798/E-MTAB-6798/Files/3040sTS.Mouse.Brain.12.5.Male.sorted.bam" ./

The error is

Session Stop  (Error: Server aborted session: No such file or directory)

I also send email to EBI four days ago. However, I still cannot get their reply. Could anyone help me? Thank you!

[Michael]

I have tested and concluded that there is a problem with Aspera download from BioStudies (ENA and BioStudies are technically different databases). Maybe there is a misconfiguration of their Aspera server. The user bsaspera is not accepted and the user era-fasp can log in but cannot see the files. Download via FTP is working though.

You can also download the original uploaded fastq files from ENA if you prefer Aspera.

To see the ENA links, go to: https://www.ebi.ac.uk/ena/browser/view/SAMEA4671623?show=reads Then click "Show column selection" and select Fastq_aspera or submitted_aspera.

Then you will get the aspera links

ascp -P33001 -i .aspera/connect/etc/asperaweb_id_dsa.openssh --host=fasp.ebi.ac.uk --user=era-fasp --mode=recv  /vol1/fastq/ERR258/003/ERR2588373/ERR2588373.fastq.gz .

or

 ascp -P33001 -i .aspera/connect/etc/asperaweb_id_dsa.openssh --host=fasp.ebi.ac.uk --user=era-fasp --mode=recv /vol1/run/ERR258/ERR2588373/3460sTS.Mouse.Heart.10.5.Female.fastq.gz .

I am sorry that this is a bit cumbersome, but possibly the best you can do for now. Regarding the response time expect 4 to 8 weeks! (even we as data brokers have to wait very long now) EBI support is swamped and massively understaffed at the moment unfortunately. That is why I have chimed in on this request.

[ruiyan_hou]

Thank you very much for your quick reply! It is very useful.

[Aster]

Confirmed this workaround works. Given ascp script from ArrayExpress doesn't work. And after I switch to the related ENA ID, it works like charm.