RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.hlfWb9/RM_1457805.WedOct291646062025
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: 1761781565
Database = /dev/shm/rModeler.hlfWb9/GCA_019693545.1_ASM1969354v1 
  - Sequences = 8639
  - Bases = 37735205
  - N50 = 21170
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  199656-213903 |                                                   [ 1 ]
  185409-199655 |                                                   [  ]
  171162-185408 |                                                   [ 1 ]
  156915-171161 |                                                   [ 1 ]
  142668-156914 |                                                   [  ]
  128421-142667 |                                                   [  ]
  114174-128420 |                                                   [ 2 ]
  99928-114174  |                                                   [ 3 ]
  85681-99927   |                                                   [ 7 ]
  71434-85680   |                                                   [ 24 ]
  57187-71433   |                                                   [ 36 ]
  42940-57186   |                                                   [ 79 ]
  28693-42939   |                                                   [ 155 ]
  14446-28692   |**                                                 [ 355 ]
  200-14446     |************************************************** [ 7975 ]

Storage Throughput = excellent ( 1087.50 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37735057 bp ( 37669608 non ambiguous )
   - Num Contigs Represented = 8639
   - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 560 raw families identified
   - RepeatScout: Running filtering stage.. 552 families remaining
   - RepeatScout: 00:03:29 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 539 families... 00:01:48 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 83 contained, found in 00:00:04 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:04 (hh:mm:ss) Elapsed Time
Round Time: 00:05:34 (hh:mm:ss) Elapsed Time : 455 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (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...
       4934 repeats masked totaling 1987662 bp(s).
   - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10020520 bp
       Num Contigs Represented = 2102
       Non ambiguous bp:
             Initial: 10005599 bp
             After Masking: 7958699 bp
             Masked: 20.46 % 
 -- Input Database Coverage: 10020520 bp out of 37735205 bp ( 26.55 % )
Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2231328
Comparison Time: 00:10:48 (hh:mm:ss) Elapsed Time, 4585 HSPs Collected
Number of families returned by RECON: 1280
Round Time: 00:12:08 (hh:mm:ss) Elapsed Time : 3 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       16018 repeats masked totaling 6632612 bp(s).
   - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27714496 bp
       Num Contigs Represented = 6619
       Non ambiguous bp:
             Initial: 27663968 bp
             After Masking: 20874747 bp
             Masked: 24.54 % 
 -- Input Database Coverage: 37735016 bp out of 37735205 bp ( 100.00 % )
Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 22676745
Comparison Time: 00:43:13 (hh:mm:ss) Elapsed Time, 32522 HSPs Collected
Number of families returned by RECON: 4879
Round Time: 00:46:37 (hh:mm:ss) Elapsed Time : 39 families discovered.

RepeatScout/RECON discovery complete: 497 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.hlfWb9/RM_1457805.WedOct291646062025
# 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: 00:02:32 (hh:mm:ss) Elapsed Time


Program Time: 01:06:51 (hh:mm:ss) Elapsed Time