fastq-dump -X 1 -Z SRR1553591 Error

[ShakySion]

Hello,

Per title, final doctor.py check reads OK for all except fastq-dump -X 1 -Z SRR1553591:

Followed the step-by-step installation instructions and things went relatively smoothly up to this point. When printing the command directly, I get this:

So I assumed that it was similar in nature to

• Problems with fastq-dump (Failed to call external services) #200

Though since I'm an absolute newbie to this, when it gets to the point of adding the sra's bin to the path in .bashrc , I've got no clue how to do that.

So I guess I'm looking for two things here, 1: is the problem the same in nature/solution, and 2. if it is how can I fix it in a step-by-step process?

Thanks for your help!

[ialbert]

The commands to install the official version of the sratools would be:

# Go to bin directory
cd ~/bin

# Download the software
wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz

# Unpack the software 
tar -zxvf sratoolkit.current-ubuntu64.tar.gz

# Add the new directory to the path
echo 'export PATH=~/bin/sratoolkit.2.11.2-ubuntu64/bin:$PATH' >> ~/.bashrc

restart the terminal and check wich version of fastq-dump is found

which fastq-dump

[ShakySion]

Huzzah! Thank you for your help! Worked like a charm!

[d2mcbrid]

Just a note on this. I encountered a similar issue (Linux subsystem on Windows 10). I did the step-by-step installation, reached this point, but after I performed the above, I wasn't able to use the conda command from my terminal. Long story short, when adding the new directory to the path, I had to use the ">>" command, not the ">" command to avoid overwriting the existing path. Hope this saves headaches for someone in the future.

[ialbert]

Yes, correct, I apologize for the typo, the >> is the append. I have now corrected the above

[ialbert]

There is an automated script now that installs sratools separately, which may be merged into the main install:

#200 (reply in thread)