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EVM
Overview
The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.
Version r2012-06-25 is available on the CSF.
Restrictions on use
This software is opensource.
Set up procedure
Please load the modulefile:
module load apps/binapps/evm/r2012-06-25
You may also require perl:
module load apps/gcc/perl/5.16.3
Running the application
Please do not run EVM on the login node. Work should be submitted to batch.
Serial batch job submission
- Make sure you have the required modulefiles loaded
- Ensure you have a weights file, the contents of which are driven by the software you have used to predict genes. For example:
ABINITIO_PREDICTION AUGUSTUS 1 ABINITIO_PREDICTION GeneMark 1
- Create a batch submission script containing all the stages you need to run. For example:
#!/bin/bash #$ -S /bin/bash #$ -cwd ### The above uses the current directory. All relevant files should be in the directory. #$ -V ### The above inherits the user environment from the login node so that commands can be found. partition_EVM_inputs.pl --genome AF300_all.fa --gene_predictions gene_predictions.gff3 --segmentSize=100000 \ --overlapSize=10000 --partition_listing partitions_list.out write_EVM_commands.pl --genome AF300_all.fa --weights ~/scratch/wt.txt --gene_predictions gene_predictions.gff3 \ --output_file_name evm.out --partitions partitions_list.out >commands.list execute_EVM_commands.pl commands.list | tee run.log recombine_EVM_partial_outputs.pl --partitions partitions_list.out --output_file_name evm.out convert_EVM_outputs_to_GFF3.pl --partitions partitions_list.out --output evm.out --genome AF300_all.fa
- Submit the job:
qsub scriptname
Parallel batch job submission
Not currently supported for EVM on the CSF.