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paoloshasta / shasta

De novo assembly from Oxford Nanopore reads.
https://paoloshasta.github.io/shasta/
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filesystem error: cannot create directory: Permission denied [ShastaRun] #39

Closed handesome closed 1 month ago

handesome commented 1 month ago

Hi! Thank you for developing the shasta!when I run ./shasta-Linux-0.11.1 --input /data/work/SRR17180611.fasta --config Nanopore-May2022 Shasta Release 0.11.1 2024-Oct-16 15:11:50.127747 filesystem error: cannot create directory: Permission denied [ShastaRun] I'm a beginner,could anyone give some suggestion?Thanks!

colindaven commented 1 month ago

I'm not the dev, but I think you are trying to run shasta from a directory you cannot write to.

Try going to a big directory on a storage you can write to.

Then do something like

/mnt/programs/shasta-Linux-0.11.1 --input /data/work/SRR17180611.fasta --config Nanopore-May2022

It could be that you need to copy /data/work/SRR17180611.fasta to your local (writable) directory and retry this.

kokyriakidis commented 1 month ago

Hi @handesome!

If you do not specify the output assembly directory, Shasta will try to write it's output to a folder named ShastaRun in your currect working directory. As @colindaven noted, probably you do not have permissions to write in your currect working directory.

You can add the option --assemblyDirectory to specify where to store the output of Shasta.

handesome commented 1 month ago

Hi！Thank you for quick reply!Now I got it!Thanks again!