fastq-dump error

Question

[maedeyousefzade96]

Hi there.

when I run fastq-dump :

./fastq-dump --stdout -X 2 SRRXXXXX

it shows this error :

Failed to call external services

How can I solve this problem?

Thanks so much.

[Ram]

Have you Googled the error message and tried solutions from the GitHub issues that are shown as search results?

[seidel]

Have you configured it correctly? Can you post the results of: vdb-config -i

[GenoMax]

Save yourself some trouble. Search with SRRXXXX (use actual accession) at EBI-ENA and download the fastq data directly.

[maedeyousefzade96]

Thank you very much. But I need to download the subset from the SRR file. Is it possible through the EBI-ENA?

[GenoMax]

Like -X option from fastq-dump? Then no since ENA only links full files.

Answer 1

[Sukjun Kim]

It seems that you cannot access network in your Linux system.

Check your internet connection first. 'ping' command will tell you whether you are connected to the internet.

$ ping www.google.com
PING www.google.com (216.58.197.196) 56(84) bytes of data.
64 bytes from nrt13s48-in-f196.1e100.net (216.58.197.196): icmp_seq=1 ttl=114 time=63.3 ms
64 bytes from nrt13s48-in-f196.1e100.net (216.58.197.196): icmp_seq=2 ttl=114 time=58.3 ms
64 bytes from nrt13s48-in-f196.1e100.net (216.58.197.196): icmp_seq=3 ttl=114 time=61.5 ms
64 bytes from nrt13s48-in-f196.1e100.net (216.58.197.196): icmp_seq=4 ttl=114 time=62.9 ms

$ fastq-dump SRR000001  # It works well

It will show an error otherwise,

$ ping www.google.com
ping: socket: Operation not permitted

$ fastq-dump SRR000001
Failed to call external services

[maedeyousefzade96]

Thank you very much. Yes, I checked the network access, and it was not a problem.