search

CAMI-challenge / CAMISIM

CAMISIM: Simulating metagenomes and microbial communities
https://data.cami-challenge.org/participate
Apache License 2.0
177 stars 37 forks source link

Some problems occur when I run “python metagenomesimulation.py defaults/mini_config.ini” #162

Closed fanqiedantang closed 1 year ago

fanqiedantang commented 1 year ago

Hi， I want to design a dataset with different complexities by camisim. However,I met some problems when i was trying to run the commond in the wiki. command:

python metagenomesimulation.py defaults/mini_config.ini

problem: image I would appreciated it if you can give me any useful information and suggestion ! Thank you !

YunyunGao374 commented 1 year ago

can you send me the command of your mini_config.ini?

AlphaSquad commented 1 year ago

Hi, it seems to me from this small excerpt that you are running CAMISIM not from its directory. The mini_config.ini references relative paths and it seems like you are running the script from your /usr/bin/ directory, but the rest of CAMISIM is not located there - you will need to adapt the paths to absolute paths in the mini_config.ini, as well as in the genome_to_id.tsv file it references if you want to do that.

fanqiedantang commented 1 year ago

Thank you for your reply ! However，after my inspection, I confirm that I am working under the camisim path. The result of command 'ls' is as follows: image

Hi, it seems to me from this small excerpt that you are running CAMISIM not from its directory. The mini_config.ini references relative paths and it seems like you are running the script from your /usr/bin/ directory, but the rest of CAMISIM is not located there - you will need to adapt the paths to absolute paths in the mini_config.ini, as well as in the genome_to_id.tsv file it references if you want to do that.

fanqiedantang commented 1 year ago

can you send me the command of your mini_config.ini?

Thank you for your help.My mini_config.ini is the default. image

AlphaSquad commented 1 year ago

Strange. Though the config is not entirely the default - the output directory is /out instead of out, but I don't really see how that could cause the error. You did not change the metadata/genome_to_id files either?

fanqiedantang commented 1 year ago

Strange. Though the config is not entirely the default - the output directory is /out instead of out, but I don't really see how that could cause the error. You did not change the metadata/genome_to_id files either?

Yes, I haven't changed any files.

AlphaSquad commented 1 year ago

Could you, just to be sure, try another output folder than /out?

AlphaSquad commented 1 year ago

Closing this due to inactivity, please re-open if you tried a different output folder and still encouter errors