Microbial eukaryotes are integral components of natural microbial communities and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, eukaryotic genomes shoould be recovered from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. EukRep is a kmer- and SVM-based strategy for eukaryotic sequence identification from environmental samples.

References:

• Patrick T. West, Alexander J. Probst, Igor V. Grigoriev, Brian C. Thomas, and Jillian F. Banfield, "Genome-reconstruction for eukaryotes from complex natural microbial communities", bioRxiv 171355; doi: https://doi.org/10.1101/171355

• EukRep Github page

• Module Name: EukRep (see the modules page for more information)
• Implemented as a Singularity container
• Singlethreaded
• Unusual environment variables set
  • EUKREP_HOME  installation directory
  • EUKREP_BIN       executable directory
  • EUKREP_TESTS  directory that stores a test script and test data
  • EUKREP_SRC      directory that contains the downloaded source code
  Interactive job
  Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

  Allocate an interactive session and run the program. Sample session:

  [user@biowulf]$ sinteractive --mem=4g
  [user@@cn3316 ~]$ module load EukRep
  

  From this point, the current installation provides several options. For exaample, just typing

  [user@@cn3316 ~]$EukRep
  Singularity EukRep_cpu.sqsh:>
  

  will bring the user to the EukRep container environment. Typing

  [user@@cn3316 ~]$EukRep python -h
  usage: python [option] ... [-c cmd | -m mod | file | -] [arg] ...
  Options and arguments (and corresponding environment variables):
  -b     : issue warnings about str(bytes_instance), str(bytearray_instance)
           and comparing bytes/bytearray with str. (-bb: issue errors)
  -B     : don't write .pyc files on import; also PYTHONDONTWRITEBYTECODE=x
  -c cmd : program passed in as string (terminates option list)
  -d     : debug output from parser; also PYTHONDEBUG=x
  -E     : ignore PYTHON* environment variables (such as PYTHONPATH)
  -h     : print this help message and exit (also --help)
  -i     : inspect interactively after running script; forces a prompt even
           if stdin does not appear to be a terminal; also PYTHONINSPECT=x
  ...
  

  will display the usage message, together with a list of available options. Finally, the following command will run an EukRep test:

  [user@@cn3316 ~]$ EukRep python $EUKREP_TESTS/EukRep_tests.py
  ...
  ------------------------------------------------------------
  Prediction tests to be performed on 13 total sequences
  Test sequences located in /usr/local/apps/EukRep/20180308/tests/test_sequences/test_scaffolds.fa
  ------------------------------------------------------------
  
  Running test predictions with 3mers...
  Expect the following sequences to be predicted to be eukaryotic:
  test_seqeunce_1
  test_sequence_2
  test_sequence_4
  test_sequence_5
  test_sequence_6
  test_sequence_7
  test_sequence_8
  test_sequence_9
  test_sequence_10
  test_sequence_11
  test_sequence_12
  test_sequence_13
  The following sequences were predicted to be eukaryotic:
  test_seqeunce_1
  test_sequence_2
  test_sequence_4
  test_sequence_5
  test_sequence_6
  test_sequence_7
  test_sequence_8
  test_sequence_9
  test_sequence_10
  test_sequence_11
  test_sequence_12
  test_sequence_13
  
  Running test predictions with 4mers...
  Expect the following sequences to be predicted to be eukaryotic:
  test_sequence_2
  test_sequence_5
  test_sequence_12
  The following sequences were predicted to be eukaryotic:
  test_sequence_2
  test_sequence_5
  test_sequence_12
  
  Running test predictions with 5mers...
  Expect the following sequences to be predicted to be eukaryotic:
  test_sequence_3
  test_sequence_5
  The following sequences were predicted to be eukaryotic:
  test_sequence_3
  test_sequence_5
  
  Running test predictions with 6mers...
  Expect the following sequences to be predicted to be eukaryotic:
  test_sequence_3
  test_sequence_5
  The following sequences were predicted to be eukaryotic:
  test_sequence_3
  test_sequence_5
  
  EukRep prediction appears to be in working order
  
  [user@cn3144 ~]$ exit
  salloc.exe: Relinquishing job allocation 46116226
  [user@biowulf ~]$
  

  Batch job
  Most jobs should be run as batch jobs.

  Create a batch input file (e.g. EukRep.sh). For example:

  #!/bin/bash
  module load EukRep
  EukRep python $EUKREP_TESTS/EukRep_tests.py
  

  Submit this job using the Slurm sbatch command.

  sbatch [--cpus-per-task=#] [--mem=#] EukRep.sh