RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.tZ5GRB/RM_4267.ThuSep111444582025
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: 1757627096
Database = /dev/shm/rModeler.tZ5GRB/GCA_025767665.1_ASM2576766v1 
  - Sequences = 725
  - Bases = 15031017
  - N50 = 85537
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  504795-540817 |                                                   [ 1 ]
  468774-504795 |                                                   [  ]
  432753-468774 |                                                   [  ]
  396732-432753 |                                                   [  ]
  360711-396732 |                                                   [ 1 ]
  324690-360711 |                                                   [  ]
  288669-324690 |                                                   [ 1 ]
  252647-288668 |                                                   [ 2 ]
  216626-252647 |                                                   [ 2 ]
  180605-216626 |                                                   [ 7 ]
  144584-180605 |                                                   [ 8 ]
  108563-144584 |                                                   [ 9 ]
  72542-108563  |**                                                 [ 27 ]
  36521-72542   |*****                                              [ 62 ]
  500-36521     |************************************************** [ 605 ]

Storage Throughput = excellent ( 1642.51 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 15030940 bp ( 14495452 non ambiguous )
   - Num Contigs Represented = 725
   - 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.. : 21 raw families identified
   - RepeatScout: Running filtering stage.. 21 families remaining
   - RepeatScout: 00:01:02 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 20 families... 00:00:10 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:14 (hh:mm:ss) Elapsed Time : 18 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       262 repeats masked totaling 122126 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10365888 bp
       Num Contigs Represented = 529
       Non ambiguous bp:
             Initial: 10034359 bp
             After Masking: 9838923 bp
             Masked: 1.95 % 
 -- Input Database Coverage: 10365888 bp out of 15031017 bp ( 68.96 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 214185
Comparison Time: 00:07:00 (hh:mm:ss) Elapsed Time, 5696 HSPs Collected
Number of families returned by RECON: 1245
Round Time: 00:07:23 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 35031017


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 35031017 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...
       155 repeats masked totaling 69203 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4664972 bp
       Num Contigs Represented = 262
       Non ambiguous bp:
             Initial: 4461013 bp
             After Masking: 4363952 bp
             Masked: 2.18 % 
 -- Input Database Coverage: 15030860 bp out of 15031017 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 46056
Comparison Time: 00:02:26 (hh:mm:ss) Elapsed Time, 891 HSPs Collected
Number of families returned by RECON: 349
Round Time: 00:02:34 (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.tZ5GRB/RM_4267.ThuSep111444582025
# 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: 00:11:18 (hh:mm:ss) Elapsed Time