zero byte files in sratoolkit.3.0.1-ubuntu64
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9 days ago
Nemo • 0

I have downloaded sratoolkit for ubuntu. After getting the tar file and unzip it, I added the bin path to the Path variables as well. When I run which fastq-dump, it correctly identifies the path. However, when I run vdb-config -i or vdb-config --interactive nothing happens. It is the same with other commands. When I look into the directory, most of the files have zero byte. I have vdb-config with zero byte, vdb-conifg.3 with zero byte, and vdb-config.3.0.1 with 6,110 KB. What do these mean?

Does this mean I should run vdb-config.3.0.1 -i?

Sorry, if I am asking naive question.

fastq sra-toolkit rna-seq • 295 views
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Run vdb-config -i to create an initial config to store data.

Save yourself some trouble and get direct fastq download links by using sra-explorer instead of fastq-dump : Post on how to use sra-explorer : find SRA and FastQ download URLs in a couple of clicks

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Yes I knew about the vdb-config -i, that bringing up an interactive environment you can change the directory to store data. But my problem is that when I run the command nothing happens.

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Are you working in a text terminal? As I recall without X11 that should still produce a text based GUI that allows you do the config. If that is not working then perhaps you have a corrupt download. Try downloading again.

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I am using ubuntu terminal on windows machine.

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That should not matter. You should still see the config dialog if the program is working.

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yes it does not work. I tried with fasterq-dump command too but same as vdb-config command, nothing happens. I also tried to download it gain but all the files are the same as before, so no issue with downloading. Do you think it can be related to zero byte files? I have added an image of folder content here. enter image description here

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