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pachterlab / sleuth

Differential analysis of RNA-Seq
http://pachterlab.github.io/sleuth
GNU General Public License v3.0
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device is out of space after executing multiple kallisto quant #249

Open eilalan opened 3 years ago

eilalan commented 3 years ago

Hello,

I am executing 

kallisto quant -t 8 -i local_kallisto_index_file -o  local_folder_align_out  file_name_1 file_name_2

for large number of samples on cloud machine. After every completed execution, the results are copied from the machine and deleted.

The execution is firing a space error after multiple quant execution. What are the other files that fill up the space? I have noticed that there is --tmp switch. Where is this tmp folder? I am running multiple quant in parallel. Is it a unique folder for each execution?

Thanks, Eila

eilalan commented 3 years ago

can someone take a look and let me know how to clean the machine after an execution from all the tmp files. Thanks eilalan

mschilli87 commented 3 years ago

Did you look for them by yourself? Something as simple as

find / -ctime 0 -user $(whoami) 2>/dev/null | less -S

would show you all files belonging to your user created in the last 24 hours. Even without knowing anything about kallisto, this might help you find those files. Especially if you did not run anything else but kallisto on that system in that time period.

Since scanning the entire file system (/) might take a long time, I would start with some educated guess like

find /tmp ~ <path-to-project-dir> -ctime 0 -user $(whoami) 2>/dev/null | less -S

to only look in likely places.