RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.xbthjA/RM_590880.FriSep120435422025
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: 1757676942
Database = /dev/shm/rModeler.xbthjA/GCA_035078465.1_MYCT-0997-2021 
  - Sequences = 360
  - Bases = 14661824
  - N50 = 105451
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  306288-328130 |                                                   [ 1 ]
  284446-306287 |                                                   [ 1 ]
  262604-284445 |                                                   [  ]
  240762-262603 |                                                   [ 2 ]
  218920-240761 |                                                   [  ]
  197078-218919 |*                                                  [ 4 ]
  175236-197077 |                                                   [ 1 ]
  153394-175235 |**                                                 [ 10 ]
  131552-153393 |**                                                 [ 10 ]
  109710-131551 |***                                                [ 13 ]
  87868-109709  |*****                                              [ 21 ]
  66026-87867   |****                                               [ 18 ]
  44184-66025   |********                                           [ 32 ]
  22342-44183   |************                                       [ 49 ]
  501-22342     |************************************************** [ 198 ]

Storage Throughput = excellent ( 1560.42 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14661723 bp ( 14640011 non ambiguous )
   - Num Contigs Represented = 360
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 43 raw families identified
   - RepeatScout: Running filtering stage.. 40 families remaining
   - RepeatScout: 00:01:01 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 35 families... 00:00:18 (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: 00:01:22 (hh:mm:ss) Elapsed Time : 34 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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       563 repeats masked totaling 240523 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10036483 bp
       Num Contigs Represented = 282
       Non ambiguous bp:
             Initial: 10015011 bp
             After Masking: 9654087 bp
             Masked: 3.60 % 
 -- Input Database Coverage: 10036483 bp out of 14661824 bp ( 68.45 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 91378
Comparison Time: 00:06:05 (hh:mm:ss) Elapsed Time, 4107 HSPs Collected
Number of families returned by RECON: 1075
Round Time: 00:06:24 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 34661824


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34661824 bp
   - Sequence extraction : 00:00:01 (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...
       243 repeats masked totaling 95135 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4625215 bp
       Num Contigs Represented = 145
       Non ambiguous bp:
             Initial: 4624975 bp
             After Masking: 4478711 bp
             Masked: 3.16 % 
 -- Input Database Coverage: 14661698 bp out of 14661824 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 17766
Comparison Time: 00:02:12 (hh:mm:ss) Elapsed Time, 738 HSPs Collected
Number of families returned by RECON: 267
Round Time: 00:02:26 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 34 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.xbthjA/RM_590880.FriSep120435422025
# 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: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:10:20 (hh:mm:ss) Elapsed Time