RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.y1P0Bn/RM_51623.TueSep90449432025
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: 1757418582
Database = /dev/shm/rModeler.y1P0Bn/GCA_006535965.1_ASM653596v1 
  - Sequences = 213
  - Bases = 22937368
  - N50 = 219537
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  908029-972740 |                                                   [ 1 ]
  843319-908029 |                                                   [  ]
  778609-843319 |                                                   [  ]
  713899-778609 |                                                   [ 1 ]
  649189-713899 |                                                   [ 1 ]
  584479-649189 |                                                   [  ]
  519769-584479 |                                                   [ 1 ]
  455058-519768 |                                                   [ 1 ]
  390348-455058 |*                                                  [ 4 ]
  325638-390348 |*                                                  [ 3 ]
  260928-325638 |******                                             [ 13 ]
  196218-260928 |*****                                              [ 11 ]
  131508-196218 |**********                                         [ 23 ]
  66798-131508  |*********************                              [ 46 ]
  2088-66798    |************************************************** [ 108 ]

Storage Throughput = excellent ( 1629.88 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22937280 bp ( 22929995 non ambiguous )
   - Num Contigs Represented = 213
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 11 raw families identified
   - RepeatScout: Running filtering stage.. 11 families remaining
   - RepeatScout: 00:00:20 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 10 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 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: 00:00:27 (hh:mm:ss) Elapsed Time : 8 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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       164 repeats masked totaling 46012 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10017281 bp
       Num Contigs Represented = 148
       Non ambiguous bp:
             Initial: 10014376 bp
             After Masking: 9955758 bp
             Masked: 0.59 % 
 -- Input Database Coverage: 10017281 bp out of 22937368 bp ( 43.67 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 46056
Comparison Time: 00:03:55 (hh:mm:ss) Elapsed Time, 1639 HSPs Collected
Number of families returned by RECON: 623
Round Time: 00:04:07 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 42937368


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42937368 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...
       280 repeats masked totaling 62350 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 12919919 bp
       Num Contigs Represented = 168
       Non ambiguous bp:
             Initial: 12915539 bp
             After Masking: 12832695 bp
             Masked: 0.64 % 
 -- Input Database Coverage: 22937200 bp out of 22937368 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 77028
Comparison Time: 00:05:24 (hh:mm:ss) Elapsed Time, 2547 HSPs Collected
Number of families returned by RECON: 826
Round Time: 00:05:40 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 12 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.y1P0Bn/RM_51623.TueSep90449432025
# 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: 00:00:05 (hh:mm:ss) Elapsed Time


Program Time: 00:10:19 (hh:mm:ss) Elapsed Time