Create a Clade Project

For this exercise 10 Dehalococcoides genomes with the file extension fasta should be in the directory $HOME/miga_genomes/dehalo. This will be the case if you followed the instructions in the section Get Example Data. Otherwise you will have to make adjustments to the commands below.

This exercise takes approximately three and a half minutes to run interactively.

If you need to, log in and start MIGA CLI using the method given in on AWS (Setup a MiGA Instance).

Create a directory for your project in the miga-data directory, move into it and initialize a clade project:

mkdir $HOME/miga-data/dehalo
cd $HOME/miga-data/dehalo
miga new -P . -t clade

The -t argument is needed to specify what kind of project you are running. Acceptable types are :

• genomes for the genomes from isolates

• clade for genomes of closely related species

For this example, we are using closely related genomes (expected ANI >= 90%), so we choose clade.

It is not necessary to add a reference database to a clade project. The genomes submitted will be compared among themselves.

Add your data set to the MiGA project. In doing this, turn off mytaxa scan, as in the command below. Here the -t flag specifies that the data being uploaded are genomes and the -i flag specifies that they are already assembled.

miga add -P . -t genome -i assembly $HOME/miga-data/miga_genomes/dehalo/*.fna -m run_mytaxa_scan=false

Launch the daemon to start MiGA processing your data:

miga daemon start -P . --shutdown-when-done

The shutdown-when-done argument automatically stops the daemon when processing is complete. After the job starts, you can display the project information with the command:

miga about -P .

Also after the job starts, you can display the dataset information:

miga ls -P . -i

And you can monitor its progress by entering:

miga ls -P . -p

which should return something like:

name                                raw_reads  trimmed_reads  read_quality  trimmed_fasta  assembly  cds   essential_genes  ssu   mytaxa  mytaxa_scan  distances  taxonomy  stats
----                                ---------  -------------  ------------  -------------  --------  ---   ---------------  ---   ------  -----------  ---------  --------  -----
  GCF_000011905_1_ASM1190v1_genomic  -          -              -             -              done      done  done             done  done    done         queued     queued    queued
 GCF_000341655_1_ASM34165v1_genomic  -          -              -             -              done      done  done             done  done    done         queued     queued    queued
 GCF_000341695_1_ASM34169v1_genomic  -          -              -             -              done      done  done             done  done    done         done       done      done
 GCF_000830925_1_ASM83092v1_genomic  -          -              -             -              done      done  done             done  done    done         done       done      done
GCF_001010485_1_ASM101048v1_genomic  -          -              -             -              done      done  done             done  done    done         done       done      done
GCF_001547795_1_ASM154779v1_genomic  -          -              -             -              done      done  done             done  done    done         done       done      done
GCF_001610775_1_ASM161077v1_genomic  -          -              -             -              done      done  done             done  done    done         done       done      done
GCF_001889305_1_ASM188930v1_genomic  -          -              -             -              done      done  done             done  done    done         done       done      done
GCF_002007845_1_ASM200784v1_genomic  -          -              -             -              done      done  done             done  done    done         queued     queued    queued
GCF_004684285_1_ASM468428v1_genomic  -          -              -             -              done      done  done             done  done    done         queued     queued    queued

When all entries in the stats column read "done," the project is finished.

If you used the ---shutdown_when_done flag, you can also check if the project is done by listing the contents of the daemon directory:

ls daemon

If a file ending in pid is present, the daemon is still running.

If you did not use the --shutdown-when-done arguement when starting the daemon, you can stop it with:

miga daemon stop -P .

See the section "Exploring Results" for how to access the results of your clade project.