RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.2d5jPn/RM_3705006.FriSep121852432025
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: 1757728362
Database = /dev/shm/rModeler.2d5jPn/GCA_051397035.1_GA10_9 
  - Sequences = 212
  - Bases = 38463161
  - N50 = 632154
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1757123-1882596 |                                                   [ 2 ]
  1631650-1757122 |                                                   [  ]
  1506177-1631649 |                                                   [  ]
  1380704-1506176 |                                                   [  ]
  1255232-1380704 |                                                   [ 2 ]
  1129759-1255231 |                                                   [ 2 ]
  1004286-1129758 |                                                   [ 1 ]
  878813-1004285  |*                                                  [ 3 ]
  753340-878812   |*                                                  [ 3 ]
  627868-753340   |**                                                 [ 6 ]
  502395-627867   |****                                               [ 12 ]
  376922-502394   |*                                                  [ 3 ]
  251449-376921   |****                                               [ 12 ]
  125976-251448   |******                                             [ 20 ]
  504-125976      |************************************************** [ 146 ]

Storage Throughput = excellent ( 1642.47 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38463145 bp ( 38462936 non ambiguous )
   - Num Contigs Represented = 212
   - 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.. : 21 raw families identified
   - RepeatScout: Running filtering stage.. 20 families remaining
   - RepeatScout: 00:00:38 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:07 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:49 (hh:mm:ss) Elapsed Time : 16 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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       167 repeats masked totaling 65049 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10018383 bp
       Num Contigs Represented = 113
       Non ambiguous bp:
             Initial: 10018272 bp
             After Masking: 9940385 bp
             Masked: 0.78 % 
 -- Input Database Coverage: 10018383 bp out of 38463161 bp ( 26.05 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 42486
Comparison Time: 00:03:50 (hh:mm:ss) Elapsed Time, 1982 HSPs Collected
Number of families returned by RECON: 797
Round Time: 00:03:59 (hh:mm:ss) Elapsed Time : 0 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       460 repeats masked totaling 96043 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28444722 bp
       Num Contigs Represented = 184
       Non ambiguous bp:
             Initial: 28444624 bp
             After Masking: 28308286 bp
             Masked: 0.48 % 
 -- Input Database Coverage: 38463105 bp out of 38463161 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 328455
Comparison Time: 00:14:45 (hh:mm:ss) Elapsed Time, 13630 HSPs Collected
Number of families returned by RECON: 3577
Round Time: 00:15:18 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 27 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.2d5jPn/RM_3705006.FriSep121852432025
# 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: 00:20:13 (hh:mm:ss) Elapsed Time