RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.YLllDV/RM_4045087.FriSep121531152025
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: 1757716274
Database = /dev/shm/rModeler.YLllDV/GCA_045529425.1_TL_RV_CBS748.79 
  - Sequences = 2616
  - Bases = 35005573
  - N50 = 37175
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  178720-191472 |                                                   [ 2 ]
  165969-178720 |                                                   [  ]
  153217-165968 |                                                   [ 3 ]
  140466-153217 |                                                   [ 5 ]
  127714-140465 |                                                   [ 3 ]
  114963-127714 |                                                   [ 5 ]
  102211-114962 |                                                   [ 11 ]
  89460-102211  |                                                   [ 12 ]
  76708-89459   |                                                   [ 14 ]
  63957-76708   |*                                                  [ 39 ]
  51205-63956   |*                                                  [ 68 ]
  38454-51205   |**                                                 [ 96 ]
  25702-38453   |*****                                              [ 190 ]
  12951-25702   |*********                                          [ 357 ]
  200-12951     |************************************************** [ 1811 ]

Storage Throughput = excellent ( 1653.28 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 35005470 bp ( 34825816 non ambiguous )
   - Num Contigs Represented = 2616
   - 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.. 19 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 16 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:00 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:00 (hh:mm:ss) Elapsed Time
Round Time: 00:00:45 (hh:mm:ss) Elapsed Time : 14 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       150 repeats masked totaling 22327 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10063331 bp
       Num Contigs Represented = 832
       Non ambiguous bp:
             Initial: 10015491 bp
             After Masking: 9972600 bp
             Masked: 0.43 % 
 -- Input Database Coverage: 10063331 bp out of 35005573 bp ( 28.75 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 370230
Comparison Time: 00:05:56 (hh:mm:ss) Elapsed Time, 2244 HSPs Collected
Number of families returned by RECON: 687
Round Time: 00:06:11 (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 : 00:00:02 (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...
       501 repeats masked totaling 73706 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 24942059 bp
       Num Contigs Represented = 1898
       Non ambiguous bp:
             Initial: 24810245 bp
             After Masking: 24681253 bp
             Masked: 0.52 % 
 -- Input Database Coverage: 35005390 bp out of 35005573 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2141415
Comparison Time: 00:17:39 (hh:mm:ss) Elapsed Time, 9226 HSPs Collected
Number of families returned by RECON: 2701
Round Time: 00:18:08 (hh:mm:ss) Elapsed Time : 6 families discovered.

RepeatScout/RECON discovery complete: 21 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.YLllDV/RM_4045087.FriSep121531152025
# 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: 00:25:09 (hh:mm:ss) Elapsed Time