Question: Sra-toolkit: Prefetch error
0
gravatar for saadleeshehreen
8 months ago by
saadleeshehreen60 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 • 900 views
ADD COMMENTlink modified 8 months ago by piet1.7k • written 8 months ago by saadleeshehreen60

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 8 months ago by Sej Modha4.2k

I tried. But still the same error message

ADD REPLYlink written 8 months ago by saadleeshehreen60

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

Have you done this configuration for conda version?

ADD REPLYlink written 8 months ago by genomax67k

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

/.vdb-config:cannot execute binary file
ADD REPLYlink written 8 months ago by saadleeshehreen60

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 8 months ago by genomax67k
0
gravatar for piet
8 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 8 months ago by piet1.7k

I tried that as well. Same error message was generated

ADD REPLYlink written 8 months ago by saadleeshehreen60

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 8 months ago by piet1.7k
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