RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.10M35b/RM_3393656.SunNov21351242025
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: 1762120284
Database = /dev/shm/rModeler.10M35b/GCA_049640115.1_ASM4964011v1 
  - Sequences = 209
  - Bases = 21214104
  - N50 = 285247
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  873445-935795 |                                                   [ 1 ]
  811096-873445 |                                                   [  ]
  748747-811096 |                                                   [ 2 ]
  686397-748746 |                                                   [ 1 ]
  624048-686397 |                                                   [  ]
  561699-624048 |                                                   [ 2 ]
  499350-561699 |                                                   [ 1 ]
  437000-499349 |*                                                  [ 3 ]
  374651-437000 |*                                                  [ 4 ]
  312302-374651 |*                                                  [ 3 ]
  249953-312302 |****                                               [ 12 ]
  187603-249952 |**                                                 [ 7 ]
  125254-187603 |******                                             [ 16 ]
  62905-125254  |************                                       [ 31 ]
  556-62905     |************************************************** [ 126 ]

Storage Throughput = excellent ( 1107.36 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 21213989 bp ( 21213689 non ambiguous )
   - Num Contigs Represented = 209
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 15 raw families identified
   - RepeatScout: Running filtering stage.. 13 families remaining
   - RepeatScout: 00:01:31 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 13 families... 00:00:06 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:44 (hh:mm:ss) Elapsed Time : 12 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 00:00:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       285 repeats masked totaling 61522 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10037995 bp
       Num Contigs Represented = 133
       Non ambiguous bp:
             Initial: 10037695 bp
             After Masking: 9961332 bp
             Masked: 0.76 % 
 -- Input Database Coverage: 10037995 bp out of 21214104 bp ( 47.32 % )
Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 48516
Comparison Time: 00:07:40 (hh:mm:ss) Elapsed Time, 3713 HSPs Collected
Number of families returned by RECON: 1621
Round Time: 00:08:25 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 41214104


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 41214104 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       736 repeats masked totaling 128884 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 11175914 bp
       Num Contigs Represented = 146
       Non ambiguous bp:
             Initial: 11175914 bp
             After Masking: 11028110 bp
             Masked: 1.32 % 
 -- Input Database Coverage: 21213909 bp out of 21214104 bp ( 100.00 % )
Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 61776
Comparison Time: 00:08:59 (hh:mm:ss) Elapsed Time, 3909 HSPs Collected
Number of families returned by RECON: 1921
Round Time: 00:09:28 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 14 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.10M35b/RM_3393656.SunNov21351242025
# 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: 00:00:12 (hh:mm:ss) Elapsed Time


Program Time: 00:19:49 (hh:mm:ss) Elapsed Time