Hi there, I am trying to retrieve sequencing data from ENA using the Aspera client and following the tutorial:
Fast download of FASTQ files from the European Nucleotide (ENA)
The tutorial has been really helpful and I followed each step. I get a download.txt file which is a list of items looking like:
ascp -QT -l 300m -P33001 -i $HOME/Applications/Aspera Connect.app/Contents/Resources/asperaweb_id_dsa.openssh email@example.com:/vol1/fastq/SRR898/002/SRR8989702/SRR8989702_1.fastq.gz .
I then followed the tutorial and ran:
while read LIST; do $LIST; done < download.txt
This leads to either two errors
Startup failed, exit ascp: no remote host specified
-bash: $LIST: ambiguous redirect
I also tried running:
And get a
permission denied error.
I'm new to this and haven't found a solution yet.
What are you doing differently to get the two errors?
If I hit return after
doI tend to get the second error and if I don't the first one. Thanks!
I am getting following error while downloading fastq files with ascp
Please guide me in this regard
The command runs smoothly on my machine. Can you try:
Just wanted to mention that the problem persists even after specifying the home directory with
Hello, did you ever figure out what caused the issue? I encountered the exact same issue while running on server (let's call this server A):
The funny thing is, the exact same command works just fine in my local Linux PC:
So I was thinking it might be a server-related issue, but I can't think of any reason why. I also confirmed that in a different server (call it server B), the command works OK. So it got to be an issue in server A, but I didn't change any configuration, etc., so I'm not sure why I'm seeing this problem. Server A is connected to Internet for sure (I can download stuff such as
$ git clone). Any help would be much appreciated!
I would talk to the server admins and discuss potential problems. It is obviously a specific problem with connection on that particilar server. Maybe some kind of firewall that is in place or ports that are not open, idk.