Question: Problems with SRA: curl: (9) Server denied you to change to the given directory
1
gravatar for gabriel.hideki
18 days ago by
gabriel.hideki10 wrote:

Good evening, everyone.

Following instructions of the Biostar Handbook, I tried to download an SRA dataset through this command:

wonderdump -X 10000 --split-files SRR1972739

The file was not downloaded and I got the following message on my Windows Bash terminal:

curl: (9) Server denied you to change to the given directory

Does anyone know how to proceed in this situation? I have just started studying bioinformatics, I'm still learning the basic concepts and any observations you have would be welcome.

Thank you all!

software error • 122 views
ADD COMMENTlink modified 17 days ago by Philipp Bayer6.5k • written 18 days ago by gabriel.hideki10

gabriel.hideki : I am going to suggest that you open a new issue at biostar handbook's GitHub site here.

Based on @Philipp's comment below others are likely to run into this pretty soon. NCBI is moving most of their data to cloud storage and some accession numbers seem to be running into problems trying to download data from SRA. Example in Biostar handbook is likely one of them.

ADD REPLYlink written 17 days ago by genomax74k
1
gravatar for Philipp Bayer
17 days ago by
Philipp Bayer6.5k
Australia/Perth/UWA
Philipp Bayer6.5k wrote:

I've had this recently too, where the official ftp didn't have a file the European or UK counterpart had.

Sometimes the raw fastq works then:

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/009/SRR1972739/SRR1972739_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/009/SRR1972739/SRR1972739_2.fastq.gz

(Got this link from https://ewels.github.io/sra-explorer/# )

or try this script to download from the European ENA: https://github.com/wwood/ena-fast-download

ADD COMMENTlink written 17 days ago by Philipp Bayer6.5k
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