RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.tRoN5G/RM_4082267.WedFeb112006502026
Search Engine = rmblast 2.14.1+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1770869210
Database = /dev/shm/rModeler.tRoN5G/GCA_004337875.1_UKP15.v0 
  - Sequences = 125
  - Bases = 9402105
  - N50 = 1190318
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1208715-1295034 |                                                   [ 2 ]
  1122396-1208714 |                                                   [ 1 ]
  1036077-1122395 |                                                   [  ]
  949758-1036076  |                                                   [ 1 ]
  863439-949757   |*                                                  [ 3 ]
  777120-863438   |                                                   [  ]
  690801-777119   |                                                   [  ]
  604482-690800   |                                                   [  ]
  518163-604481   |                                                   [ 1 ]
  431844-518162   |                                                   [  ]
  345525-431843   |                                                   [ 1 ]
  259206-345524   |                                                   [  ]
  172887-259205   |                                                   [ 2 ]
  86568-172886    |*                                                  [ 3 ]
  250-86568       |*************************************************  [ 111 ]

Storage Throughput = excellent ( 1627.25 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 9401988 bp ( 9095088 non ambiguous )
   - Num Contigs Represented = 125
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 7 raw families identified
   - RepeatScout: Running filtering stage.. 4 families remaining
   - RepeatScout: 00:00:35 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 3 families... 00:00:03 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:40 (hh:mm:ss) Elapsed Time : 3 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       43 repeats masked totaling 10597 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9401988 bp
       Num Contigs Represented = 125
       Non ambiguous bp:
             Initial: 9095088 bp
             After Masking: 9007566 bp
             Masked: 0.96 % 
 -- Input Database Coverage: 9401988 bp out of 9402105 bp ( 100.00 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 60726
Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 1014 HSPs Collected
Number of families returned by RECON: 343
Round Time: 00:05:28 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 3 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.tRoN5G/RM_4082267.WedFeb112006502026
# Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib
#   - 18011 proteins
# Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib
#   - 26292 consensus sequences
  - Looking for simple/tandem and low complexity sequences..
  - Looking for similarity to known repeat proteins..
  - Looking for similarity to known repeat consensi..

Classification Time: 00:00:04 (hh:mm:ss) Elapsed Time


Program Time: 00:06:12 (hh:mm:ss) Elapsed Time