RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.uvXtz8/RM_847856.FriSep120324592025
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: 1757672699
Database = /dev/shm/rModeler.uvXtz8/GCA_032356705.1_MYCT-1531-2021 
  - Sequences = 346
  - Bases = 14788742
  - N50 = 116200
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  298073-319329 |                                                   [ 1 ]
  276818-298073 |                                                   [  ]
  255563-276818 |                                                   [ 2 ]
  234308-255563 |                                                   [  ]
  213053-234308 |                                                   [  ]
  191797-213052 |*                                                  [ 4 ]
  170542-191797 |                                                   [ 2 ]
  149287-170542 |**                                                 [ 9 ]
  128032-149287 |****                                               [ 17 ]
  106777-128032 |*****                                              [ 19 ]
  85521-106776  |***                                                [ 12 ]
  64266-85521   |******                                             [ 26 ]
  43011-64266   |*****                                              [ 22 ]
  21756-43011   |***********                                        [ 42 ]
  501-21756     |************************************************** [ 190 ]

Storage Throughput = excellent ( 1642.63 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14788641 bp ( 14786832 non ambiguous )
   - Num Contigs Represented = 346
   - 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.. : 49 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... 00:00:18 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:24 (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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       547 repeats masked totaling 229582 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10026704 bp
       Num Contigs Represented = 264
       Non ambiguous bp:
             Initial: 10025405 bp
             After Masking: 9687220 bp
             Masked: 3.37 % 
 -- Input Database Coverage: 10026704 bp out of 14788742 bp ( 67.80 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 81810
Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 4030 HSPs Collected
Number of families returned by RECON: 1018
Round Time: 00:06:33 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 34788742


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34788742 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...
       292 repeats masked totaling 108074 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4761916 bp
       Num Contigs Represented = 163
       Non ambiguous bp:
             Initial: 4761406 bp
             After Masking: 4602944 bp
             Masked: 3.33 % 
 -- Input Database Coverage: 14788620 bp out of 14788742 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 19701
Comparison Time: 00:02:20 (hh:mm:ss) Elapsed Time, 798 HSPs Collected
Number of families returned by RECON: 308
Round Time: 00:02:30 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 35 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.uvXtz8/RM_847856.FriSep120324592025
# 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: 00:10:34 (hh:mm:ss) Elapsed Time