RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.l03bWi/RM_412501.FriSep121936582025
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: 1757731017
Database = /dev/shm/rModeler.l03bWi/GCA_051397335.1_GA2_2 
  - Sequences = 215
  - Bases = 38819975
  - N50 = 1032145
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2763472-2960828 |                                                   [ 1 ]
  2566117-2763472 |                                                   [  ]
  2368762-2566117 |                                                   [  ]
  2171407-2368762 |                                                   [  ]
  1974052-2171407 |                                                   [  ]
  1776697-1974052 |                                                   [ 1 ]
  1579342-1776697 |                                                   [  ]
  1381986-1579341 |*                                                  [ 4 ]
  1184631-1381986 |*                                                  [ 4 ]
  987276-1184631  |*                                                  [ 5 ]
  789921-987276   |**                                                 [ 7 ]
  592566-789921   |                                                   [ 3 ]
  395211-592566   |*                                                  [ 5 ]
  197856-395211   |*****                                              [ 17 ]
  501-197856      |************************************************** [ 168 ]

Storage Throughput = excellent ( 1529.64 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38819823 bp ( 38819735 non ambiguous )
   - Num Contigs Represented = 215
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 24 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:00:38 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 21 families... 00:00:08 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:50 (hh:mm:ss) Elapsed Time : 20 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       230 repeats masked totaling 85680 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10017990 bp
       Num Contigs Represented = 98
       Non ambiguous bp:
             Initial: 10017972 bp
             After Masking: 9919289 bp
             Masked: 0.99 % 
 -- Input Database Coverage: 10017990 bp out of 38819975 bp ( 25.81 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 43365
Comparison Time: 00:03:49 (hh:mm:ss) Elapsed Time, 1542 HSPs Collected
Number of families returned by RECON: 732
Round Time: 00:04:02 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       637 repeats masked totaling 166475 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28801779 bp
       Num Contigs Represented = 176
       Non ambiguous bp:
             Initial: 28801709 bp
             After Masking: 28592885 bp
             Masked: 0.73 % 
 -- Input Database Coverage: 38819769 bp out of 38819975 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 356590
Comparison Time: 00:15:02 (hh:mm:ss) Elapsed Time, 14965 HSPs Collected
Number of families returned by RECON: 3775
Round Time: 00:15:37 (hh:mm:ss) Elapsed Time : 7 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.l03bWi/RM_412501.FriSep121936582025
# 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: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:20:36 (hh:mm:ss) Elapsed Time