Changing temp_directory in config file

[CassandraHjo]

I am looking to run multiple simulations at once on a cluster, and therefore want to have different temp directories. I have tried the following two methods:

• Change the name of the temp_directory in the config.ini file to something else (for instance from /tmp (like in the default) to /tmp2)
• Change the name of the temp_directory by giving the full path to the "new" temp_directory

When doing this I get this error: ERROR: [Validator 18394365136] Directory does not exist: '/tmp2' I therefore tried to make the temp directory inside the CAMISIM folder before starting the simulation, but I still get the same error message.

I am unsure if using the same temp_directory for two simulations (same input genomes, metadata and number of samples) running at once will cause any problems, but if so: how do I change the temp_directory in the config file?

[AlphaSquad]

Hi, in contrast to the out directory, CAMISIM will create individual folders under the /tmp directory, so it should not be a problem to have multiple CAMISIM runs with the same /tmp directory. That is also the reason why changing the directory to /tmp2 does not work - CAMISIM does not create the temp_directory directory but only folders "below" that. Also note that since the path starts with the / it is an absolute path/in the root path of your file system, so you probably are unable to create a new /tmp2 directory without haveing root access. If you want the temp_directory to be within the CAMISIM path (which I would not necessarily recommend), you would have to choose tmp (without the leading /) as a relative path

[TakacsBertalan]

Hi! I am experiencing a similar error. Could you tell me how you managed to solve it? My root /tmp directory doesn't have enough space for CAMISIM, so I specified an existing directory on an external hard drive with more than enough space, with it's absolute path. Still, I keep getting the following message: "ERROR: [NcbiTaxonomy] Directory does not exist: '/tmp/tmp_36zttyq/delnodes.dmp'"

It seems like, even though I specified a new tmp, CAMISIM still tries to use the old one. I tried to specify the path as a relative path, but it gave the same result. I would appreciate any help

[CassandraHjo]

I solved my problem by defining the full path to the temp directory. In my case I also needed to create the directory before I ran the pipeline as "CAMISIM does not create the temp_directory directory but only folders "below" that."

[TakacsBertalan]

Thank you for the quick answer! Interesting, I think I am doing the same, I still get the error. I will open a new issue. Thanks for the help!

EDIT: For anyone running into this issue. I managed to solve it by unpacking my taxdump.tar.gz file, and specifying the correct path in the config file.