RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.lCRTkt/RM_3741398.FriSep121854442025
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: 1757728483
Database = /dev/shm/rModeler.lCRTkt/GCA_051397045.1_GA10_13 
  - Sequences = 341
  - Bases = 38384483
  - N50 = 279742
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  848700-909286 |                                                   [ 1 ]
  788115-848700 |                                                   [  ]
  727530-788115 |                                                   [ 3 ]
  666944-727529 |                                                   [ 1 ]
  606359-666944 |                                                   [  ]
  545774-606359 |                                                   [ 2 ]
  485189-545774 |*                                                  [ 7 ]
  424603-485188 |**                                                 [ 8 ]
  364018-424603 |*                                                  [ 5 ]
  303433-364018 |**                                                 [ 8 ]
  242848-303433 |******                                             [ 26 ]
  182262-242847 |****                                               [ 19 ]
  121677-182262 |******                                             [ 27 ]
  61092-121677  |**********                                         [ 40 ]
  507-61092     |************************************************** [ 194 ]

Storage Throughput = excellent ( 1346.62 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38384393 bp ( 38383934 non ambiguous )
   - Num Contigs Represented = 341
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 17 raw families identified
   - RepeatScout: Running filtering stage.. 16 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 14 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:45 (hh:mm:ss) Elapsed Time : 14 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...
       111 repeats masked totaling 17404 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10015083 bp
       Num Contigs Represented = 169
       Non ambiguous bp:
             Initial: 10014996 bp
             After Masking: 9985794 bp
             Masked: 0.29 % 
 -- Input Database Coverage: 10015083 bp out of 38384483 bp ( 26.09 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 47895
Comparison Time: 00:03:57 (hh:mm:ss) Elapsed Time, 1804 HSPs Collected
Number of families returned by RECON: 751
Round Time: 00:04:11 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 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...
       509 repeats masked totaling 75347 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28369258 bp
       Num Contigs Represented = 299
       Non ambiguous bp:
             Initial: 28368886 bp
             After Masking: 28252420 bp
             Masked: 0.41 % 
 -- Input Database Coverage: 38384341 bp out of 38384483 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 377146
Comparison Time: 00:14:58 (hh:mm:ss) Elapsed Time, 13549 HSPs Collected
Number of families returned by RECON: 3610
Round Time: 00:15:30 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.lCRTkt/RM_3741398.FriSep121854442025
# 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: 00:20:33 (hh:mm:ss) Elapsed Time