RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.kHEIAI/RM_1629792.FriSep120431442025
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: 1757676703
Database = /dev/shm/rModeler.kHEIAI/GCA_035078385.1_MYCT-2752-2021 
  - Sequences = 366
  - Bases = 14660449
  - N50 = 91450
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  325359-348564 |                                                   [ 1 ]
  302155-325359 |                                                   [  ]
  278951-302155 |                                                   [  ]
  255747-278951 |                                                   [ 2 ]
  232543-255747 |                                                   [ 1 ]
  209338-232542 |                                                   [ 1 ]
  186134-209338 |*                                                  [ 4 ]
  162930-186134 |*                                                  [ 6 ]
  139726-162930 |**                                                 [ 9 ]
  116522-139726 |**                                                 [ 10 ]
  93317-116521  |***                                                [ 14 ]
  70113-93317   |*******                                            [ 28 ]
  46909-70113   |********                                           [ 35 ]
  23705-46909   |**************                                     [ 56 ]
  501-23705     |************************************************** [ 199 ]

Storage Throughput = excellent ( 1640.94 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14660348 bp ( 14658550 non ambiguous )
   - Num Contigs Represented = 366
   - 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.. : 55 raw families identified
   - RepeatScout: Running filtering stage.. 52 families remaining
   - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 46 families... 00:00:24 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 9 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:29 (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 : 00:00:00 (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...
       639 repeats masked totaling 235550 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10015995 bp
       Num Contigs Represented = 295
       Non ambiguous bp:
             Initial: 10014928 bp
             After Masking: 9673577 bp
             Masked: 3.41 % 
 -- Input Database Coverage: 10015995 bp out of 14660449 bp ( 68.32 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 87153
Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 4471 HSPs Collected
Number of families returned by RECON: 1068
Round Time: 00:06:36 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 34660449


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34660449 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...
       339 repeats masked totaling 110780 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4644273 bp
       Num Contigs Represented = 145
       Non ambiguous bp:
             Initial: 4643542 bp
             After Masking: 4479543 bp
             Masked: 3.53 % 
 -- Input Database Coverage: 14660268 bp out of 14660449 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 17020
Comparison Time: 00:02:18 (hh:mm:ss) Elapsed Time, 776 HSPs Collected
Number of families returned by RECON: 279
Round Time: 00:02:28 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 38 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.kHEIAI/RM_1629792.FriSep120431442025
# 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: 00:10:41 (hh:mm:ss) Elapsed Time