RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.RbKIuB/RM_2651395.MonSep81710312025
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: 1757376631
Database = /dev/shm/rModeler.RbKIuB/GCA_002215765.1_Cryp_neof_AD1_83a_V1 
  - Sequences = 498
  - Bases = 18636876
  - N50 = 155223
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  692931-742355 |                                                   [ 1 ]
  643507-692930 |                                                   [  ]
  594084-643507 |                                                   [  ]
  544660-594083 |                                                   [ 1 ]
  495236-544659 |                                                   [  ]
  445813-495236 |                                                   [ 1 ]
  396389-445812 |                                                   [  ]
  346965-396388 |                                                   [ 4 ]
  297542-346965 |                                                   [ 4 ]
  248118-297541 |                                                   [ 7 ]
  198694-248117 |                                                   [ 7 ]
  149271-198694 |*                                                  [ 8 ]
  99847-149270  |***                                                [ 29 ]
  50423-99846   |*****                                              [ 41 ]
  1000-50423    |************************************************** [ 395 ]

Storage Throughput = excellent ( 1542.75 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18636738 bp ( 18636573 non ambiguous )
   - Num Contigs Represented = 498
   - 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.. : 45 raw families identified
   - RepeatScout: Running filtering stage.. 45 families remaining
   - RepeatScout: 00:00:19 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 42 families... 00:00:08 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 6 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:30 (hh:mm:ss) Elapsed Time : 36 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       568 repeats masked totaling 290136 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10013407 bp
       Num Contigs Represented = 300
       Non ambiguous bp:
             Initial: 10013405 bp
             After Masking: 9713819 bp
             Masked: 2.99 % 
 -- Input Database Coverage: 10013407 bp out of 18636876 bp ( 53.73 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 98790
Comparison Time: 00:04:39 (hh:mm:ss) Elapsed Time, 2618 HSPs Collected
Number of families returned by RECON: 642
Round Time: 00:04:55 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 38636876


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38636876 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       689 repeats masked totaling 302874 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8623275 bp
       Num Contigs Represented = 292
       Non ambiguous bp:
             Initial: 8623112 bp
             After Masking: 8311396 bp
             Masked: 3.61 % 
 -- Input Database Coverage: 18636682 bp out of 18636876 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 84255
Comparison Time: 00:03:54 (hh:mm:ss) Elapsed Time, 1633 HSPs Collected
Number of families returned by RECON: 563
Round Time: 00:04:08 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 41 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.RbKIuB/RM_2651395.MonSep81710312025
# 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: 00:00:11 (hh:mm:ss) Elapsed Time


Program Time: 00:09:44 (hh:mm:ss) Elapsed Time