#!/bin/bash --login
########## SBATCH Lines for Resource Request ##########
#SBATCH --time=4:00:00 # limit of wall time - how long the job will run
#SBATCH --nodes=1 # number of different nodes - exact number or range
#SBATCH --ntasks=1 # number of tasks - how many tasks (nodes) you require
#SBATCH --cpus-per-task=12 # number of CPUs (cores) per task
#SBATCH --mem-per-cpu=2G # memory required per allocated CPU (or core)
#SBATCH --job-name assemble # job name for easier identification
#SBATCH -A colej
########## Command Lines to Run ##########
mkdir ~/test_assemble
cd ~/test_assemble
singularity shell ~/MiGA << EOF
miga new -P ~/test_assemble -t genomes
miga add -P ~/test_assemble -t genome -i trimmed_reads_single ~/miga_genomes/a_capsulatum/A_capsulatum_reads.fasta
time miga daemon start -t -P . --shutdown-when-done
exit
EOF
A report on the assembled genome can be obtained with:
less ~/test_assemble/data/07.annotation/01.function/01.essential/A_capsulatum_reads.ess/log
which reveals:
! Collection: dupont_2012
! Essential genes found: 105/111.
! Completeness: 94.6%.
! Contamination: 2.7%.
! Multiple copies:
! 2 tRNA-synt_1d: tRNA synthetases class I (R).
! 2 GrpE: GrpE.
! 2 TIGR00436: era: GTP-binding protein Era.
! Missing genes:
! TIGR00389: glyS_dimeric: glycine--tRNA ligase.
! TIGR00408: proS_fam_I: proline--tRNA ligase.
! TIGR00471: pheT_arch: phenylalanine--tRNA ligase, beta subunit.
! TIGR00775: NhaD: Na+/H+ antiporter, NhaD family.
! TIGR00810: secG: preprotein translocase, SecG subunit.
! TIGR02387: rpoC1_cyan: DNA-directed RNA polymerase, gamma subunit.
The assembled genome can be retrieved as ~/test_assemble/data/05.assembly/A_capsulatum_reads.AllContigs.fna
Times reported for this project were (real = wall time):
| _ | Time |
|---|---|
| real | 8m42.971s |
| user | 8m26.007s |
| sys | 0m05.480s |