Download of FASTQ files from the European Nucleotide Archive (ENA) using Aspera

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 era-fasp@fasp.sra.ebi.ac.uk:/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

Or:

-bash: $LIST: ambiguous redirect

I also tried running:

$HOME/Applications/Aspera Connect.app/Contents/Resources/asperaweb_id_dsa.openssh

And get a permission denied error.

I’m new to this and haven’t found a solution yet.

Thanks for reporting the issue. I could reproduce the error and think it is due to the whitespace in the name of the Aspera folder. Could you try to rename Aspera Connect into something without whitespace e.g. AsperaConnect.app, then adjust the download command accordingly and try again. I guess that is Mac-specific because (wisely) Linux does not use a whitespace in the folder name. I Did it on my machine and the errors disappeared, still I got a time-out message. Not sure if this is due to an error at ENA which happens at times, so if you cannot download, maybe wait a day and try again. Connection errors are rather frequent in my experience. I will double check when I’ve access to my workstation tomorrow.

==> Edit: The whitespacing is not an issue if properly escaped. I updated the command in the tutorial so that the awk command does not mess it up. It should be fine towards that initial error you got.