RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.QYYsUr/RM_846434.FriSep120324442025
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: 1757672683
Database = /dev/shm/rModeler.QYYsUr/GCA_032356685.1_MYCT-1551-2021 
  - Sequences = 357
  - Bases = 14755040
  - N50 = 101369
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  338102-362217 |                                                   [ 1 ]
  313988-338102 |                                                   [  ]
  289874-313988 |                                                   [ 1 ]
  265759-289873 |                                                   [  ]
  241645-265759 |                                                   [ 1 ]
  217531-241645 |                                                   [  ]
  193417-217531 |*                                                  [ 7 ]
  169302-193416 |                                                   [ 1 ]
  145188-169302 |                                                   [ 4 ]
  121074-145188 |****                                               [ 19 ]
  96960-121074  |******                                             [ 26 ]
  72845-96959   |******                                             [ 27 ]
  48731-72845   |*****                                              [ 22 ]
  24617-48731   |***********                                        [ 45 ]
  503-24617     |************************************************** [ 203 ]

Storage Throughput = excellent ( 1628.02 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14754989 bp ( 14740267 non ambiguous )
   - Num Contigs Represented = 357
   - 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.. : 51 raw families identified
   - RepeatScout: Running filtering stage.. 46 families remaining
   - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 38 families... 00:00:29 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 5 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:34 (hh:mm:ss) Elapsed Time : 33 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...
       580 repeats masked totaling 226255 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10008442 bp
       Num Contigs Represented = 281
       Non ambiguous bp:
             Initial: 10007132 bp
             After Masking: 9677100 bp
             Masked: 3.30 % 
 -- Input Database Coverage: 10008442 bp out of 14755040 bp ( 67.83 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 90525
Comparison Time: 00:06:10 (hh:mm:ss) Elapsed Time, 3546 HSPs Collected
Number of families returned by RECON: 989
Round Time: 00:06:28 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 34755040


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34755040 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       264 repeats masked totaling 133710 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4746504 bp
       Num Contigs Represented = 146
       Non ambiguous bp:
             Initial: 4733092 bp
             After Masking: 4538293 bp
             Masked: 4.12 % 
 -- Input Database Coverage: 14754946 bp out of 14755040 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 18721
Comparison Time: 00:02:16 (hh:mm:ss) Elapsed Time, 914 HSPs Collected
Number of families returned by RECON: 324
Round Time: 00:02:25 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 33 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.QYYsUr/RM_846434.FriSep120324442025
# 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: 00:10:35 (hh:mm:ss) Elapsed Time