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RepeatModeler.md

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RepeatModeler

Module: Bio::EnsEMBL::EGPipeline::PipeConfig::RepeatModeler_conf

Pipeline for building de-novo repeat libraries using RepeatModeler utility.

Prerequisites

A registry file with the locations of the core database server(s).

How to run

# REPEAT_MODELLER_OPTIONS='-max_seq_length 19000000' # or whatever

init_pipeline.pl Bio::EnsEMBL::EGPipeline::PipeConfig::RepeatModeler_conf \
  $($CMD details script) \
  -pipeline_tag  "_${RUN_TAG}" \
  -hive_force_init 1 \
  -registry $REG_FILE \
  -results_dir $RESULTS_DIR \
  -species $SPECIES \
  ${REPEAT_MODELLER_OPTIONS} \
  -do_clustering 1 \
  2> $OUT_DIR/init.stderr \
  1> $OUT_DIR/init.stdout

SYNC_CMD=$(cat $OUT_DIR/init.stdout | grep -- -sync'$' | perl -pe 's/^\s*//; s/"//g')
# should get something like
#   beekeeper.pl -url $url -sync

LOOP_CMD=$(cat $OUT_DIR/init.stdout | grep -- -loop | perl -pe 's/^\s*//; s/\s*#.*$//; s/"//g')
# should get something like
#   beekeeper.pl -url $url -reg_file $REG_FILE -loop

$SYNC_CMD 2> $OUT_DIR/sync.stderr 1> $OUT_DIR/sync.stdout
$LOOP_CMD 2> $OUT_DIR/loop.stderr 1> $OUT_DIR/loop.stdout

Parameters / Options

option default value meaning
-species species to process, several -species options are possible
-results_dir directory to store results to
-min_slice_length 5000 ignore scaffolds that are shorter then this value
-max_seq_length 10_000_000 maximum length for a single scaffold, scaffolds will be splitted if exciding this value
-max_seqs_per_file 10_000 maximum number of scaffolds to be processed in a chnuck (by a single RepeatModeler) instance
-do_clustering 0 deal with redundancy of the final library, using CDHit-EST clustering
-do_filtering 0 remove repeat models that are found in CDSs (details)
-repeatmodeler_dir Path to the directory containing the RepeatModeler executables
-blast_engine ncbi which BLAST program to use; options are 'ncbi' or 'wublast'

Output

Each chunked portion of the genome will produce a repeat library file. These are simply concatenated to produce a single file in the ${RESULTS_DIR} directory, named <SPECIES>.rm.lib, where <SPECIES> is the species production_name. There is likely to be some redundancy here, particularly for large genomes that have correspondingly large numbers of chunk files. This isn't ideal, but our main goal is to repeat mask the genome (for which redundancy doesn't matter), so the library is a means to an end, rather than an end in itself. The pipeline uses the multi-core functionality of RepeatModeler (9 cores per hive job), which makes the program faster and enables us to chunk as little as possible; but it remains a necessary evil. Use -do_clustering 1 to deal with the library redundancy.

Parts

A few generic from Common::RunnableDB.

A few from DNAFeatures.