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Over the past 24 hours, I've tried using prefetch with multiple .krt files from multiple dbGaP projects, with no success. The input and output are always of the form:
`$ .../sratoolkit.3.1.1-centos…
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- update sratoolkit to sratoolkit/3.0.1 - newer version avoids running program for configuration
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Original size: 762Mb.
Change #1: Size decreased to 369Mb.
Other ways to decrease the size:
- use alpine
- remove wget
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Hi David, I am currently running orthofinder on my pc and the program returns some errors iteratively. I am using orthofinder 2.5.4
on conda architecture right now.
Checking required programs ar…
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All of the SRA tests have been skipping because of a failure to download the necessary SRA drivers.
This started happening sometime between september 20th and october 24.
It looks like there w…
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just report
install sra toolkits i need to find these two links and they were very useful
https://ncbi.github.io/sra-tools/install_config.html
https://ncbi.github.io/sra-tools/fastq-dump.html (for …
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succeeded(108643), failed(569) 26.8762% completed. mkdir: cannot create directory '/mnt/i/jujufirst/sratoolkit.2.11.0-win64/bin/trinity_out_dir/read_partitions': Invalid argument
Error, cmd: mkd…
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Hi,
I am working on a pipeline that downloads SRR files, and to optimize the download time, I opted for your tool. However, I am encountering an issue. I have a list of 143 files, and when I run thi…
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I am currently running sratoolkit 3.1.1 and have run into the following error:
`~/anaconda3/envs/new_env/bin/fastq-dump ./PRJNA870935/raw_data/SRR21148806 -O ./PRJNA870935 --split-3 `
```
2024-…
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the downloading_from_SRA.md lesson needs to be updated. The code as is doesn't work.
One issue was resolved using current module `module load sratoolkit/3.0.2`