Problem while downloading SRR file via **ASPERA CONNECT**
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12 months ago
dpc ▴ 170

I was trying to download SRR data (SRR304976) using aspera connect. I have used the following command:

/home/deep/.aspera/connect/bin/ascp -T -k1 -i /home/deep/.aspera/connect/etc/asperaweb_id_dsa.openssh anonftp@ftp.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR304/SRR304976/SRR304976.sra /home/deep/XXXXXXX

BUT, the following result was obtained:

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

Please let me know where is the problem and how should i use aspera connect to download data effectively?

sequence next-gen SRR aspera connect • 1.7k views
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Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
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Few weeks ago NIH moved his data, I am not sure if Aspera will work, you can try the new fasterq-dump command, here are the new access https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR304976

Type    Size    Location    Name    Free Egress Access Type
run 1,004,639 Kb    NCBI    https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR304976/SRR304976.3   worldwide   anonymous
NCBI    https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR304976/SRR304976.3   worldwide   anonymous
AWS s3://sra-pub-run-1/SRR304976/SRR304976.3    s3.us-east-1    aws identity
GCP gs://sra-pub-run-1/SRR304976/SRR304976.3    gs.US   gcp identity
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Use the links available under "Data Access" tab when you open the individual runs (there are two) for this accession.

Where did you get the paths from? Are those correct in your command line?

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12 months ago
ATpoint 47k

NCBI does not offer download via Aspera anymore since they moved their files to Cloud-based storage solutions which corrently are not compatible with Aspera, see also: Aspera ascp command line utility inside prefetch call to facilitate SRA data downloading

An alternative is to download fastq directly from ENA (Fast download of FASTQ files from the European Nucleotide Archive (ENA)) but since they are currently performing data center migration most downloads are currently not possible. I suggest you download SRA files from NCBI with prefetch which is a specialized utility for this inside the sra-toolkit.

prefetch -O ./ SRR304976 will download the SRA file to the directory from which the command is launched.

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Sir, thanks for your answer . But downloading large data takes very very long time when downloaded via prefetch. Is there any faster way to download?

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Yes, ENA via Aspera but this is currently down. Nothing you can do about it. ENA data submission service disruptions 11th-27th March

This is the situation, so download with prefetch and have tea in the meantime :)

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Hi ATpoint

I have more than 70TB of WGS to download from SRA/ENA... I can see your reply about ENA via Aspera being down. however in your post here you say ENA via Aspera is the best solution.

What do you think should work best for me? P.S tried prefetch with SRAtools but it looks like random downloads fail while others dont and I need to keep rerunning failing downloads - not fun..

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Hi, that downtime was last year march, it is long over. Yes, ENA via Aspera is currently the probably fastest option I am aware of if the data you want are actually hosted at ENA and not access-restricted. I would do that if you can, and if not then prefetch. 70TB is a lot though, it will take time.

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ATpoint - thanks so much for your prompt reply!

  • The data is indeed access-restricted (I have an .ngc file from dbGAP to allow access)
  • Is the data hosted at ENA? When I look for the SRRXXXX in ENA website I get results . However, when I use sra-explorer to enter SRRXXXXX it gives me commands with nothing standing for my SRRXXXX. I understand it is probably because my data is access restricted

However, According to Shicheng Guo in this post access restricted data CAN be downloaded via aspera. Possible?

Thanks

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