Entering edit mode
3.0 years ago
NewtoBioinfo
•
0
Hello, I'm new to bioinformatics. I installed sra-tools through conda on my Mac Terminal. Then tried the prefetch tool to download SRA run data but I get the below error.
$ prefetch SRR8434837
An error occured: std::exception
If this continues to happen, please contact the SRA Toolkit at https://trace.ncbi.nlm.nih.gov/Traces/sra/
$ srapath -V
"srapath" version 2.11.0
$ srapath ERR359711
An error occured: std::exception
If this continues to happen, please contact the SRA Toolkit at https://trace.ncbi.nlm.nih.gov/Traces/sra/
Can anybody help with the next steps?
I could use wget to get the reads but then I'm not sure how to use fastq-dump after that.
Are you using a M1 CPU based mac?
machdep.cpu.brand_string: Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz machdep.cpu.brand: 0
prefetch was working with srapath verson 2.10.4. After I updated it to 2.11.0, it started giving me this error.
Ah I see. This is important information. I would suggest that you report this using the link provided above or create an issue on their GitHub site.
In the mean time you can get the fastq data directly from SRR8434837 from EBI-ENA and for ERR359711.