Submitting a Genome Project with Classification

It is also possible to request that reference genomes be classified against a reference database when the project is first run. To do this, create the new project and edit it to include a reference project database. Then add the reference genomes and start the daemon.

The following script assumes that you have installed TypeMat_Lite in $HOME/.miga_db (section "Installing_TypeMat_Lite") and that the reference sequences for this exercise are in $HOME/miga_genomes/misc.

#!/bin/bash --login
########## SBATCH Lines for Resource Request ##########
#SBATCH --time=04:00:00         # limit of wall clock time - how long the job will run (same as -t)
#SBATCH --nodes=1               # number of different nodes - could be an exact number or a range of nodes (same as -N)
#SBATCH --ntasks=18             # number of tasks - how many tasks (nodes) that you require (same as -n)
#SBATCH --cpus-per-task=2      # number of CPUs (or cores) per task (same as -c)
#SBATCH --mem-per-cpu=4G        # memory required per allocated CPU (or core) - amount of memory (in bytes)
#SBATCH --job-name class        # you can give your job a name for easier identification (same as -J)

########## Command Lines to Run ##########

mkdir ~/miga_class
cd ~/miga_class

singularity shell ~/MiGA << EOF
miga new -P . -t genomes
miga edit -P . -m ref_project=~/.miga_db/TypeMat_Lite
miga add -P . -t genome -i assembly ~/miga_genomes/misc/*.fasta -m run_mytaxa_scan=false,run_distances=true
time miga daemon start -t -P . --shutdown-when-done
exit
EOF

A summary classification can be obtained with the MiGA command:

Singularity> miga ls -P ~/miga_class/ -m tax

which returns:

Acidobacterium_capsulatum       d:Bacteria p:Acidobacteria c:Acidobacteriia o:Acidobacteriales
Acinetobacter_baumanii  d:Bacteria p:Proteobacteria c:Gammaproteobacteria
Bacillus_anthracis      d:Bacteria p:Firmicutes c:Bacilli o:Bacillales
Bacillus_cereus d:Bacteria p:Firmicutes c:Bacilli o:Bacillales
Bifidobacterium_bifidum d:Bacteria p:Actinobacteria c:Actinobacteria o:Bifidobacteriales f:Bifidobacteriaceae
Campylobacter_jejuni    d:Bacteria p:Proteobacteria c:Epsilonproteobacteria o:Campylobacterales
Cytophaga_hutchinsonii  d:Bacteria p:Bacteroidetes c:Cytophagia
Gemmatimonas_aurantiaca d:Bacteria p:Gemmatimonadetes c:Gemmatimonadetes o:Gemmatimonadales
Lacunisphaera_limnophila        d:Bacteria p:Verrucomicrobia c:Opitutae o:Opitutales

Individual *intax.txt files for each genome can be found in directory ~/miga_class/data/09.distances/05.taxonomy/. For example:

less ~/miga_class/data/09.distances/05.taxonomy/Bifidobacterium_bifidum.intax.txt

returns:

Closest relative: Bifidobacterium_scardovii_JCM_12489___DSM_13734_GCA_000770985 with AAI: 68.94928718008717.

      Rank  Taxonomy                                         P-value               Signif.
      ----  --------                                         -------               -------
      root  ?                                                0.0                   ****
    domain  Bacteria                                         0.0                   ****
    phylum  Actinobacteria                                   0.000191394343233856  ****
     class  Actinobacteria                                   0.00118380945629829   ****
     order  Bifidobacteriales                                0.0024385057063869    ****
    family  Bifidobacteriaceae                               0.0481321329836251    ***
     genus  Bifidobacterium                                  0.256907918054866     *
   species  Bifidobacterium scardovii                        0.876302544835897
subspecies  ?                                                0.960990997377189
   dataset  Bifidobacterium scardovii JCM 12489 = DSM 13734  0.965570284256043

Significance at p-value below: *0.5, **0.1, ***0.05, ****0.01.

Times reported for this project were (real = wall time):

_	Time
real	35m 44.452s
user	307m 05.617s
sys	12m 41.245s