Create a Genome Project

For this exercise 6 Psuedomonas genomes with the file extension fasta should be in the directory $HOME/miga-data/miga_genomes/pseudo. 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 3 minutes to run using 8 CPUs.

Log in and start MIGA CLI using the method for a MiGA-AWS on AWS (Setup a MiGA Instance).

From your home directory, create a new project named pseudo:

mkdir -p $HOME/miga-data/pseudo
cd $HOME/miga-data/pseudo
miga new -P . -t genomes

You can safely ignore any warning about a bind mount. The -t argument is needed to specify what kind of project you are running. Acceptable types are:

• genomes for genomes in general

• clade for closely related genomes

For this example, we are using genomes from isolates.

Add your datasets ending with fasta to the MiGA project. In doing this, turn off mytaxa scan and make sure distances is turned on, as in the command below. There must be no space after the comma(s) in the items listed for the -m flag or an error will occur. Here the -t flag specifies the type of genome being added to the project. The -i flag specifies that the datasets being uploaded are assembled genomes.

miga add -P . -t genome -i assembly $HOME/miga-data/miga_genomes/pseudo/*.fasta -m run_mytaxa_scan=false,run_distances=true

Launch the daemon to start MiGA processing your data:

miga daemon start -P . --shutdown_when_done

After the job starts, you can display the information about the job:

miga about -P .

Also after the job starts, you can list the datasets being processed by entering:

miga ls -P . -i

And you can monitor the job progress by entering:

miga ls -P . -p

This should give something like:

name           raw_reads  trimmed_reads  read_quality  trimmed_fasta  assembly  cds   essential_genes  ssu   mytaxa  mytaxa_scan  distances  taxonomy  stats
         ----  ---------  -------------  ------------  -------------  --------  ---   ---------------  ---   ------  -----------  ---------  --------  -----
P_alcaligenes  -          -              -             -              done      done  done             done  done    done         queued     queued    queued
P_fluorescens  -          -              -             -              done      done  done             done  done    done         queued     queued    queued
  P_mendocina  -          -              -             -              done      done  done             done  done    done         queued     queued    queued
     P_putida  -          -              -             -              done      done  done             done  done    done         queued     queued    queued
   P_stutzeri  -          -              -             -              done      done  done             done  done    done         done       done      done
   P_syringae  -          -              -             -              done      done  done             done  done    done         queued     queued    queued

Because the datasets submitted were assembled genomes, assembly is the first column to have entries. When all entries under the stats column read "done," processing is finished. You can also check that the project is finished by listing the files in the project daemon directory.

ls daemon

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

If you did not include --shutdown_when_done when you started the daemon and the job is finished, you can stop the daemon with the command:

miga daemon stop -P .

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