RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.BEz8Vr/RM_1471426.ThuSep110554302025
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: 1757595269
Database = /dev/shm/rModeler.BEz8Vr/GCA_023623695.1_ASM2362369v1 
  - Sequences = 650
  - Bases = 14898626
  - N50 = 84379
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  751384-805020 |                                                   [ 1 ]
  697748-751383 |                                                   [  ]
  644113-697748 |                                                   [  ]
  590477-644112 |                                                   [  ]
  536842-590477 |                                                   [ 1 ]
  483206-536841 |                                                   [  ]
  429571-483206 |                                                   [  ]
  375935-429570 |                                                   [  ]
  322300-375935 |                                                   [ 1 ]
  268664-322299 |                                                   [ 1 ]
  215029-268664 |                                                   [ 6 ]
  161393-215028 |                                                   [ 8 ]
  107758-161393 |                                                   [ 11 ]
  54122-107757  |***                                                [ 42 ]
  487-54122     |************************************************** [ 579 ]

Storage Throughput = excellent ( 1644.28 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14898525 bp ( 14598764 non ambiguous )
   - Num Contigs Represented = 650
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 29 raw families identified
   - RepeatScout: Running filtering stage.. 25 families remaining
   - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 24 families... 00:00:11 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 5 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:16 (hh:mm:ss) Elapsed Time : 19 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       335 repeats masked totaling 150810 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10236140 bp
       Num Contigs Represented = 476
       Non ambiguous bp:
             Initial: 10019924 bp
             After Masking: 9793855 bp
             Masked: 2.26 % 
 -- Input Database Coverage: 10236140 bp out of 14898626 bp ( 68.71 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 186966
Comparison Time: 00:06:50 (hh:mm:ss) Elapsed Time, 6122 HSPs Collected
Number of families returned by RECON: 1151
Round Time: 00:07:13 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 34898626


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34898626 bp
   - Sequence extraction : 00:00:00 (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...
       154 repeats masked totaling 55801 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4662341 bp
       Num Contigs Represented = 235
       Non ambiguous bp:
             Initial: 4578796 bp
             After Masking: 4488637 bp
             Masked: 1.97 % 
 -- Input Database Coverage: 14898481 bp out of 14898626 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 36315
Comparison Time: 00:02:32 (hh:mm:ss) Elapsed Time, 828 HSPs Collected
Number of families returned by RECON: 353
Round Time: 00:02:40 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 21 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.BEz8Vr/RM_1471426.ThuSep110554302025
# 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: 00:11:16 (hh:mm:ss) Elapsed Time