RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.KwrKr4/RM_3866737.WedSep101419302025
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: 1757539170
Database = /data/tmp/rModeler.KwrKr4/GCA_018154785.1_ASM1815478v1 
  - Sequences = 401
  - Bases = 19536098
  - N50 = 353446
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1055278-1130641 |                                                   [ 1 ]
  979915-1055277  |                                                   [ 1 ]
  904552-979914   |                                                   [  ]
  829190-904552   |                                                   [ 1 ]
  753827-829189   |                                                   [  ]
  678464-753826   |                                                   [ 2 ]
  603101-678463   |                                                   [ 2 ]
  527739-603101   |                                                   [ 2 ]
  452376-527738   |                                                   [ 1 ]
  377013-452375   |                                                   [ 4 ]
  301650-377012   |*                                                  [ 9 ]
  226288-301650   |*                                                  [ 10 ]
  150925-226287   |*                                                  [ 7 ]
  75562-150924    |**                                                 [ 19 ]
  200-75562       |************************************************** [ 342 ]

Storage Throughput = excellent ( 1657.67 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19536059 bp ( 19525638 non ambiguous )
   - Num Contigs Represented = 401
   - 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.. : 20 raw families identified
   - RepeatScout: Running filtering stage.. 20 families remaining
   - RepeatScout: 00:00:36 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 19 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:44 (hh:mm:ss) Elapsed Time : 15 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 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       315 repeats masked totaling 52537 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10010287 bp
       Num Contigs Represented = 236
       Non ambiguous bp:
             Initial: 10004257 bp
             After Masking: 9895673 bp
             Masked: 1.09 % 
 -- Input Database Coverage: 10010287 bp out of 19536098 bp ( 51.24 % )
Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 92235
Comparison Time: 00:05:38 (hh:mm:ss) Elapsed Time, 18289 HSPs Collected
Number of families returned by RECON: 1615
Round Time: 00:06:17 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 39536098


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39536098 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2198 repeats masked totaling 229650 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9525725 bp
       Num Contigs Represented = 228
       Non ambiguous bp:
             Initial: 9521334 bp
             After Masking: 9245545 bp
             Masked: 2.90 % 
 -- Input Database Coverage: 19536012 bp out of 19536098 bp ( 100.00 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 81003
Comparison Time: 00:04:50 (hh:mm:ss) Elapsed Time, 2643 HSPs Collected
Number of families returned by RECON: 740
Round Time: 00:05:11 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 21 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.KwrKr4/RM_3866737.WedSep101419302025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:12:18 (hh:mm:ss) Elapsed Time