RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.TCripG/RM_3727364.FriSep120308002025
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: 1757671679
Database = /data/tmp/rModeler.TCripG/GCA_032356505.1_MYCT-2184-2021 
  - Sequences = 353
  - Bases = 14841700
  - N50 = 107082
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  270809-290117 |                                                   [ 1 ]
  251502-270809 |                                                   [ 2 ]
  232195-251502 |                                                   [ 2 ]
  212888-232195 |                                                   [ 3 ]
  193581-212888 |                                                   [ 3 ]
  174273-193580 |                                                   [  ]
  154966-174273 |*                                                  [ 5 ]
  135659-154966 |**                                                 [ 11 ]
  116352-135659 |**                                                 [ 11 ]
  97045-116352  |*****                                              [ 20 ]
  77737-97044   |****                                               [ 15 ]
  58430-77737   |*****                                              [ 21 ]
  39123-58430   |********                                           [ 30 ]
  19816-39123   |***********                                        [ 42 ]
  509-19816     |************************************************** [ 187 ]

Storage Throughput = excellent ( 1203.33 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14841629 bp ( 14762806 non ambiguous )
   - Num Contigs Represented = 353
   - 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.. : 59 raw families identified
   - RepeatScout: Running filtering stage.. 52 families remaining
   - RepeatScout: 00:01:51 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 39 families... 00:00:57 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 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: 00:02:51 (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 00:00:18 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       615 repeats masked totaling 244988 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10060979 bp
       Num Contigs Represented = 272
       Non ambiguous bp:
             Initial: 10017431 bp
             After Masking: 9662837 bp
             Masked: 3.54 % 
 -- Input Database Coverage: 10060979 bp out of 14841700 bp ( 67.79 % )
Sampling Time: 00:00:23 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 85905
Comparison Time: 00:07:59 (hh:mm:ss) Elapsed Time, 3662 HSPs Collected
Number of families returned by RECON: 1019
Round Time: 00:08:32 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 34841700


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34841700 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       418 repeats masked totaling 145046 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4780586 bp
       Num Contigs Represented = 153
       Non ambiguous bp:
             Initial: 4745311 bp
             After Masking: 4547077 bp
             Masked: 4.18 % 
 -- Input Database Coverage: 14841565 bp out of 14841700 bp ( 100.00 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 19306
Comparison Time: 00:02:47 (hh:mm:ss) Elapsed Time, 849 HSPs Collected
Number of families returned by RECON: 303
Round Time: 00:03:04 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 39 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.TCripG/RM_3727364.FriSep120308002025
# 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: 00:00:09 (hh:mm:ss) Elapsed Time


Program Time: 00:14:36 (hh:mm:ss) Elapsed Time