Kallisto not able to find the index file or abundance.tsv

[swinnier]

Hello,

I downloaded Kallisto via a conda environment on my VM that uses Ubuntu, it seemed like it was installed correctly; however, when I tried to run a script that uses kallisto index and quant, I get the two errors below:

cp: cannot stat 'vol/data/kallisto_flower/SRR23422625/abundance.tsv': No such file or directory
Error: kallisto index file not found /vol/data/kallisto_flower/index

I have changed the permissions so the directory "kallisto_flower" is writable and executable, but it still does not fix these errors. I also started to download and build kallisto without a conda environment, but the required packages keep getting this error "E: Unable to locate package." I searched on Ubuntu for the packages and followed their instructions for installation, however it still did not work. Do you know what could be the source of this issue?

[Yenaled]

Those errors are due to files not being found. This doesn't appear to be an issue with kallisto; it's an issue with the script that you tried to run.

[swinnier]

I tried running Kallisto without the script and it gave me the same error. From my understanding, Kallisto was not working properly because it was not creating the index or abundance.tsv file.

…

On Sat, Sep 9, 2023 at 9:34 PM Delaney Sullivan ***@***.***> wrote: Those errors are due to files not being found. This doesn't appear to be an issue with kallisto; it's an issue with the script that you tried to run. — Reply to this email directly, view it on GitHub <#397 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQDXSIZF6FKYXVUOGFBMQW3XZURKZANCNFSM6AAAAAA4RSPTLI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Yenaled]

You'll need to show the exact commands you're running otherwise there's no way anyone can help you (we don't have access to your computer or server).