AlphaSquad
commented
5 years ago Hi, thank you for your comment. The docker container is not extensively tested, so there still might be some bugs. In this case you are missing a biom file which you would have to put in the correct path, the "mini.biom" is just an example and not provided along CAMISIM. Additionally, you have to change the path you are mounting.
"/path/to/input/directory:/input:rw"
mounts the path before the : to the path after within the docker container and probably your input is not located in the path /path/to/input/directory locally. I would kindly advise to check the docker manual for details on how to run and mount docker containers.
When running CAMISIM directly outside of a docker container, you will also need a biom profile if you want to run ./metagenome_from_profile.py. If you don't have a profile, or you want to run CAMISIM without one (using ./metagenomesimulation.py), you will need a set of genomes and their taxonomic classification and need to set the files in your config file appropriately. The default configuration is not stored under
configuration/metagenome_simulation
but under
defaults/default_config.ini
which you need to change according to your needs. For details how to do this, please refer to the wiki
ParkvilleData
HI, I have followed the update documentation but I am having trouble running CAMISAM.
Running the docker command says the mini.biom file is not available. I try entering the docker container using bash but that also gives me an error. I also try running "python metagenomesimulation.py configuration/metagenome_simulation" but it's unclear where that configuration is.. I thought it might be the config file which I have edited to suit but that doesn't work. would I be able to get some help getting this to run please?
`bshaban@6300d-111439-l:~/camisim$ sudo docker run -it -v "/path/to/input/directory:/input:rw" -v "/path/to/output/directory:/output:rw" cami/camisim:latest metagenome_from_profile.py -p /input/mini.biom -o /output NCBI database not present yet (first time used?) Downloading taxdump.tar.gz from NCBI FTP site... Done. Parsing... Loading node names... 2044492 names loaded. 249789 synonyms loaded. Loading nodes... 2044492 nodes loaded. Linking nodes... Tree is loaded. Updating database: /root/.etetoolkit/taxa.sqlite ... 2044000 generating entries... Uploading to /root/.etetoolkit/taxa.sqlite
Inserting synonyms: 245000 Inserting taxid merges: 50000 Inserting taxids: 2040000 2019-01-16 23:37:51 WARNING: [root] Max strains per OTU not set, using default (3) 2019-01-16 23:37:51 WARNING: [root] Mu and sigma have not been set, using defaults (1,2) Traceback (most recent call last): File "metagenome_from_profile.py", line 87, in
config = GG.generate_input(args) # total number of genomes and path to updated config
File "/usr/local/bin/scripts/get_genomes.py", line 283, in generate_input
tax_profile = read_taxonomic_profile(args.profile, config, args.samples)
File "/usr/local/bin/scripts/get_genomes.py", line 26, in read_taxonomic_profile
table = biom.load_table(biom_profile)
File "/usr/local/lib/python2.7/dist-packages/biom/parse.py", line 652, in load_table
with biom_open(f) as fp:
File "/usr/lib/python2.7/contextlib.py", line 17, in enter
return self.gen.next()
File "/usr/local/lib/python2.7/dist-packages/biom/util.py", line 443, in biom_open
if os.path.getsize(fp) == 0:
File "/usr/lib/python2.7/genericpath.py", line 57, in getsize
return os.stat(filename).st_size
OSError: [Errno 2] No such file or directory: '/input/mini.biom'`