RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.43MZKR/RM_417015.MonSep81350002025
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: 1757364599
Database = /dev/shm/rModeler.43MZKR/GCA_001466575.1_ASM146657v1 
  - Sequences = 132
  - Bases = 12826081
  - N50 = 384427
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  640727-686417 |                                                   [ 1 ]
  595038-640727 |                                                   [ 1 ]
  549349-595038 |*                                                  [ 2 ]
  503659-549348 |                                                   [  ]
  457970-503659 |                                                   [ 1 ]
  412281-457970 |*                                                  [ 3 ]
  366591-412280 |***                                                [ 6 ]
  320902-366591 |*                                                  [ 3 ]
  275213-320902 |*                                                  [ 2 ]
  229523-275212 |*                                                  [ 3 ]
  183834-229523 |                                                   [ 1 ]
  138145-183834 |**                                                 [ 4 ]
  92455-138144  |******                                             [ 10 ]
  46766-92455   |**********                                         [ 16 ]
  1077-46766    |************************************************** [ 79 ]

Storage Throughput = excellent ( 1676.28 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12825973 bp ( 12816720 non ambiguous )
   - Num Contigs Represented = 132
   - 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.. : 21 raw families identified
   - RepeatScout: Running filtering stage.. 20 families remaining
   - RepeatScout: 00:00:17 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 17 families... 00:00:08 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:28 (hh:mm:ss) Elapsed Time : 16 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 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       225 repeats masked totaling 71524 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10011387 bp
       Num Contigs Represented = 118
       Non ambiguous bp:
             Initial: 10004356 bp
             After Masking: 9855106 bp
             Masked: 1.49 % 
 -- Input Database Coverage: 10011387 bp out of 12826081 bp ( 78.05 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 51681
Comparison Time: 00:04:24 (hh:mm:ss) Elapsed Time, 3274 HSPs Collected
Number of families returned by RECON: 749
Round Time: 00:04:49 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 32826081


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32826081 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       66 repeats masked totaling 17199 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2814506 bp
       Num Contigs Represented = 51
       Non ambiguous bp:
             Initial: 2812284 bp
             After Masking: 2772519 bp
             Masked: 1.41 % 
 -- Input Database Coverage: 12825893 bp out of 12826081 bp ( 100.00 % )
Sampling Time: 00:00:04 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 3916
Comparison Time: 00:00:58 (hh:mm:ss) Elapsed Time, 214 HSPs Collected
Number of families returned by RECON: 96
Round Time: 00:01:02 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 17 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.43MZKR/RM_417015.MonSep81350002025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:06:25 (hh:mm:ss) Elapsed Time