RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.DmzEtO/RM_943414.FriSep120332562025
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: 1757673175
Database = /dev/shm/rModeler.DmzEtO/GCA_032356765.1_MYCT-1368-2021 
  - Sequences = 359
  - Bases = 14827447
  - N50 = 99407
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  377616-404553 |                                                   [ 1 ]
  350679-377615 |                                                   [  ]
  323743-350679 |                                                   [  ]
  296806-323742 |                                                   [ 1 ]
  269870-296806 |                                                   [  ]
  242933-269869 |                                                   [ 2 ]
  215997-242933 |                                                   [ 3 ]
  189060-215996 |                                                   [ 3 ]
  162124-189060 |                                                   [ 3 ]
  135187-162123 |*                                                  [ 8 ]
  108251-135187 |****                                               [ 18 ]
  81314-108250  |*****                                              [ 23 ]
  54378-81314   |*******                                            [ 31 ]
  27441-54377   |****************                                   [ 65 ]
  505-27441     |************************************************** [ 201 ]

Storage Throughput = excellent ( 1662.42 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14827345 bp ( 14756089 non ambiguous )
   - Num Contigs Represented = 359
   - 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 39 families... 00:00:21 (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: 00:01:26 (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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       702 repeats masked totaling 271322 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10086041 bp
       Num Contigs Represented = 280
       Non ambiguous bp:
             Initial: 10015125 bp
             After Masking: 9626144 bp
             Masked: 3.88 % 
 -- Input Database Coverage: 10086041 bp out of 14827447 bp ( 68.02 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 86736
Comparison Time: 00:05:48 (hh:mm:ss) Elapsed Time, 4272 HSPs Collected
Number of families returned by RECON: 1032
Round Time: 00:06:12 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 34827447


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34827447 bp
   - Sequence extraction : 00:00:00 (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...
       291 repeats masked totaling 134644 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4741291 bp
       Num Contigs Represented = 162
       Non ambiguous bp:
             Initial: 4740951 bp
             After Masking: 4560113 bp
             Masked: 3.81 % 
 -- Input Database Coverage: 14827332 bp out of 14827447 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 20100
Comparison Time: 00:02:30 (hh:mm:ss) Elapsed Time, 630 HSPs Collected
Number of families returned by RECON: 291
Round Time: 00:02:39 (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.DmzEtO/RM_943414.FriSep120332562025
# 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: 00:00:12 (hh:mm:ss) Elapsed Time


Program Time: 00:10:29 (hh:mm:ss) Elapsed Time