Question: Sra-toolkit: Prefetch error
0
gravatar for saadleeshehreen
14 months ago by
saadleeshehreen70 wrote:

Hi, I installed the sratoolkit from NCBI by following. While running prefetch, the following error generated. I assume something wrong with my path. How can I solve it?

  export PATH="/Network/Servers/biocldap.otago.ac.nz/Volumes/userdata/student_users/saadleeshehreen/miniconda3/bin:$PATH"
conda install -c daler sratoolkit
-bash-4.2$ which prefetch
~/miniconda3/bin/prefetch
 -bash-4.2$ prefetch https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR7768518
 Maximum file size download limit is 20,971,520KB

2018-09-05T10:36:57 prefetch.2.5.7 int: path incorrect while resolving tree within virtual file system module - 
 https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR7768518: VResolverLocal

As conda version didn't work, I tried different approach. I am a Mac user. So, downloaded the sratoolkit.2.9.2-mac64 and installed it locally. I got the following errors:

~/sratoolkit.2.9.2-mac64/bin/prefetch SRR7768518
bash: /Network/Servers/biocldap.otago.ac.nz/Volumes/userdata/student_users/saadleeshehreen/sratoolkit.2.9.2-mac64/bin/prefetch: cannot execute binary file

Any solution to solve it?

Thanks in advance.

Cheers

sratoolkit • 1.7k views
ADD COMMENTlink modified 14 months ago by piet1.7k • written 14 months ago by saadleeshehreen70

Are you sure that ~/sratoolkit.2.9.2-mac64/bin/prefetch has executable permission? Try changing the permissions using chmod 755 ~/sratoolkit.2.9.2-mac64/bin/*

ADD REPLYlink written 14 months ago by Sej Modha4.5k

I tried. But still the same error message

ADD REPLYlink written 14 months ago by saadleeshehreen70

The message about file size download limit is not an error. See this.

Have you done this configuration for conda version?

ADD REPLYlink written 14 months ago by genomax74k

After your reply I tried that but still give the following error message

/.vdb-config:cannot execute binary file
ADD REPLYlink written 14 months ago by saadleeshehreen70

You say that you downloaded the macOS executables so assuming that is correct can you do chmod a+x vdb-config and see if that allows you to execute that file? Other possibility is that you may have downloaded linux executables which will not work on macOS.

ADD REPLYlink written 14 months ago by genomax74k
0
gravatar for piet
14 months ago by
piet1.7k
planet earth
piet1.7k wrote:

prefetch https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR7768518

You have passed an URL to prefetch, but prefetch expects simply an accession number.

prefetch SRR7768518`

ADD COMMENTlink written 14 months ago by piet1.7k

I tried that as well. Same error message was generated

ADD REPLYlink written 14 months ago by saadleeshehreen70

I have tested it, and it worked fine for me. Unfortunately, there is a typo in my answer, please try without the backtick.

prefetch SRR7768518

ADD REPLYlink written 14 months ago by piet1.7k
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