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.
•
written
by
maedeyousefzade96 •
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
Thank you very much. Yes, I checked the network access, and it was not a problem.
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Have you Googled the error message and tried solutions from the GitHub issues that are shown as search results?
Have you configured it correctly? Can you post the results of: vdb-config -i
Save yourself some trouble. Search with
SRRXXXX(use actual accession) at EBI-ENA and download the fastq data directly.Thank you very much. But I need to download the subset from the SRR file. Is it possible through the EBI-ENA?
Like
-Xoption fromfastq-dump? Then no since ENA only links full files.