RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.YK3g6O/RM_2929317.MonSep81902262025
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: 1757383345
Database = /dev/shm/rModeler.YK3g6O/GCA_002864075.1_CtY66041.0 
  - Sequences = 1221
  - Bases = 14552636
  - N50 = 56447
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  276454-296180 |                                                   [ 1 ]
  256729-276454 |                                                   [  ]
  237004-256729 |                                                   [  ]
  217278-237003 |                                                   [  ]
  197553-217278 |                                                   [  ]
  177828-197553 |                                                   [ 2 ]
  158102-177827 |                                                   [ 1 ]
  138377-158102 |                                                   [ 6 ]
  118652-138377 |                                                   [ 4 ]
  98926-118651  |                                                   [ 11 ]
  79201-98926   |                                                   [ 17 ]
  59476-79201   |*                                                  [ 30 ]
  39750-59475   |**                                                 [ 47 ]
  20025-39750   |*****                                              [ 102 ]
  300-20025     |************************************************** [ 1000 ]

Storage Throughput = excellent ( 1639.92 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14552550 bp ( 13610174 non ambiguous )
   - Num Contigs Represented = 1221
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 2 raw families identified
   - RepeatScout: Running filtering stage.. 2 families remaining
   - RepeatScout: 00:00:55 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 1 families... 00:00:05 (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: 00:01:03 (hh:mm:ss) Elapsed Time : 1 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 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       13 repeats masked totaling 4078 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10682847 bp
       Num Contigs Represented = 901
       Non ambiguous bp:
             Initial: 10007571 bp
             After Masking: 9987680 bp
             Masked: 0.20 % 
 -- Input Database Coverage: 10682847 bp out of 14552636 bp ( 73.41 % )
Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 500500
Comparison Time: 00:07:55 (hh:mm:ss) Elapsed Time, 3028 HSPs Collected
Number of families returned by RECON: 1002
Round Time: 00:08:16 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 34552636


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34552636 bp
   - Sequence extraction : 00:00:00 (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...
       8 repeats masked totaling 3102 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 3869674 bp
       Num Contigs Represented = 380
       Non ambiguous bp:
             Initial: 3602574 bp
             After Masking: 3593241 bp
             Masked: 0.26 % 
 -- Input Database Coverage: 14552521 bp out of 14552636 bp ( 100.00 % )
Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 79003
Comparison Time: 00:02:30 (hh:mm:ss) Elapsed Time, 415 HSPs Collected
Number of families returned by RECON: 213
Round Time: 00:02:36 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 2 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.YK3g6O/RM_2929317.MonSep81902262025
# 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: 00:00:05 (hh:mm:ss) Elapsed Time


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