I tried that as well. Same error message was generated
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Sra-toolkit: Prefetch error
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
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piet
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saadleeshehreen
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saadleeshehreen
1 answer
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`
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Are you sure that
~/sratoolkit.2.9.2-mac64/bin/prefetchhas executable permission? Try changing the permissions usingchmod 755 ~/sratoolkit.2.9.2-mac64/bin/*I tried. But still the same error message
The message about file size download limit is not an error. See this.
Have you done this configuration for conda version?
After your reply I tried that but still give the following error message
You say that you downloaded the macOS executables so assuming that is correct can you do
chmod a+x vdb-configand 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.