Repeatmodeler - Revision history

Rf at 13:48, 20 October 2017

2017-10-20T13:48:04Z

Rf at 13:21, 20 October 2017

2017-10-20T13:21:55Z

Rf at 13:17, 20 October 2017

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Rf at 12:37, 20 October 2017

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Rf at 12:11, 20 October 2017

2017-10-20T12:11:28Z

Rf at 11:38, 20 October 2017

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Rf at 10:56, 20 October 2017

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@@ Line 93: / Line 93: @@
 * '''yeast288c-families.fa'''  - Consensus sequences for each family identified.
 * '''yeast288c-families.stk''' - Seed alignments for each family identified
 = Installation notes =

@@ Line 87: / Line 87: @@
 Round 1 is a repeat search using Repeatscout and its build_lmer_table. A series of subrounds follows.
-Next is round 2 which uses TRFMask and when finished gives the number of HSPs and then uses RECON for family definitions.
+Next is round 2 which uses TRFMask and when finished gives the number of HSPs and then uses RECON for family definitions and then it refines the family.
 = Installation notes =

@@ Line 77: / Line 77: @@
 This is only a wrapper to the blast makedatabase function, and should finish quickly depending on he size of the file of course. Yeast is small (12MB), so it was over quickly.
 = Installation notes =
@@ Line 118: / Line 128: @@
 = Links =
-* [https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bti1018 the RepeatScount paper]gg
+* [https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bti1018 the RepeatScount paper]

@@ Line 10: / Line 10: @@
   Use of uninitialized value $1 in string ne at /shelf/modulefiles/tools/RepeatModeler/1.0.10/SequenceSimilarityMatrix.pm line 273, <MATRIX> line 7
-Because it is only a warning, it should not affetc the proper running of the program. In any case, it will be repaired shortly.
+Because it is only a warning, it should not affect the proper running of the program. In any case, it will be repaired shortly.
 Here are the contents of the help manual:
@@ Line 68: / Line 68: @@
        Robert Hubley <rhubley@systemsbiology.org>
        Arian Smit <asmit@systemsbiology.org>
 = Installation notes =

← Older revision		Revision as of 12:37, 20 October 2017
Line 3:		Line 3:
	This is a sister program to RepeatMasker. It also has no publication behind it.		This is a sister program to RepeatMasker. It also has no publication behind it.

		+	= Usage =

		+	* NB always use '''-engine ncbi''' when running RepeatModeler.
		+	* NB2 There is a warning like so in the output:

−	~~= Usage =~~
−
−	~~NB always use '''-engine ncbi''' when running RepastModeler.~~
−	~~NB2 There is a warning like so in the output:~~
	Use of uninitialized value $1 in string ne at /shelf/modulefiles/tools/RepeatModeler/1.0.10/SequenceSimilarityMatrix.pm line 273, <MATRIX> line 7		Use of uninitialized value $1 in string ne at /shelf/modulefiles/tools/RepeatModeler/1.0.10/SequenceSimilarityMatrix.pm line 273, <MATRIX> line 7

@@ Line 1: / Line 1: @@
 = Introduction =
 = Usage =
 Here are the contents of the help manual:
@@ Line 97: / Line 107: @@
 This is quite similar to RepeatMasker, although there is an opportunity to manually edit '''RepModelConfig.pm.tmp''' which is more accurate and convenient than the automatic configure script. Predictably, it will only be active when the tmp extension is hived off.

← Older revision		Revision as of 11:38, 20 October 2017
Line 1:		Line 1:
	= Introduction =		= Introduction =

		+	= Usage =
		+
		+	Here are the contents of the help manual:
		+
		+	$ RepeatModeler --help
		+	No database indicated
		+
		+	NAME
		+	RepeatModeler - Model repetitive DNA
		+
		+	SYNOPSIS
		+	RepeatModeler [-options] -database <XDF Database>
		+
		+	DESCRIPTION
		+	The options are:
		+
		+	-h(elp)
		+	Detailed help
		+
		+	-database
		+	The prefix name of a XDF formatted sequence database containing the
		+	genomic sequence to use when building repeat models. The database
		+	may be created with the WUBlast "xdformat" utility or with the
		+	RepeatModeler wrapper script "BuildXDFDatabase".
		+
		+	-engine <abblast\|wublast\|ncbi>
		+	The name of the search engine we are using. I.e abblast/wublast or
		+	ncbi (rmblast version).
		+
		+	-pa #
		+	Specify the number of shared-memory processors available to this
		+	program. RepeatModeler will use the processors to run BLAST searches
		+	in parallel. i.e on a machine with 10 cores one might use 1 core for
		+	the script and 9 cores for the BLAST searches by running with "-pa
		+	9".
		+
		+	-recoverDir <Previous Output Directory>
		+	If a run fails in the middle of processing, it may be possible
		+	recover some results and continue where the previous run left off.
		+	Simply supply the output directory where the results of the failed
		+	run were saved and the program will attempt to recover and continue
		+	the run.
		+
		+	-srand #
		+	Optionally set the seed of the random number generator to a known
		+	value before the batches are randomly selected ( using Fisher Yates
		+	Shuffling ). This is only useful if you need to reproduce the sample
		+	choice between runs. This should be an integer number.
		+
		+	SEE ALSO
		+	RepeatMasker, WUBlast
		+
		+	COPYRIGHT
		+	Copyright 2005-2017 Institute for Systems Biology
		+
		+	AUTHOR
		+	Robert Hubley <rhubley@systemsbiology.org>
		+	Arian Smit <asmit@systemsbiology.org>

	= Installation notes =		= Installation notes =

← Older revision		Revision as of 10:56, 20 October 2017
Line 35:		Line 35:
	* merge-lmer-tables.prl		* merge-lmer-tables.prl
	* compare-out-to-gff.prl		* compare-out-to-gff.prl
		+
		+	== RepeatModeler itself ==
		+
		+	This is quite similar to RepeatMasker, although there is an opportunity to manually edit '''RepModelConfig.pm.tmp''' which is more accurate and convenient than the automatic configure script. Predictably, it will only be active when the tmp extension is hived off.

@@ Line 29: / Line 29: @@
 * build_lmer_table
-and also the following must be installed:
+and also the following perl scripts (using the unusual *.prl extension) must be also be installed:
 * filter-stage-1.prl

@@ Line 1: / Line 1: @@
-= Introdcuction =
+= Introduction =
-It consists of the following executables:
 * imagespread
@@ Line 9: / Line 20: @@
 * famdef
-= Installation notes =
+So all these are now available in '''/usr/local/bin''' in the nodes as well.
-'''nseg''' and '''nmerge''' (included in '''nseg''') are quite old programs coded in C by NCBI. These were installed on all machines in '''/usr/local/bin'''
+and also the following must be installed:
-Similarly RECON
+* filter-stage-1.prl