RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.GvM80H/RM_808747.FriSep121957442025
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: 1757732263
Database = /dev/shm/rModeler.GvM80H/GCA_051397475.1_GA8_1 
  - Sequences = 203
  - Bases = 38575541
  - N50 = 727673
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1640041-1757151 |*                                                  [ 3 ]
  1522931-1640040 |                                                   [  ]
  1405822-1522931 |                                                   [  ]
  1288712-1405821 |                                                   [ 1 ]
  1171603-1288712 |                                                   [ 1 ]
  1054493-1171602 |                                                   [ 2 ]
  937383-1054492  |                                                   [ 1 ]
  820274-937383   |*                                                  [ 4 ]
  703164-820273   |**                                                 [ 7 ]
  586055-703164   |***                                                [ 10 ]
  468945-586054   |*                                                  [ 5 ]
  351835-468944   |*                                                  [ 3 ]
  234726-351835   |*****                                              [ 16 ]
  117616-234725   |***                                                [ 11 ]
  507-117616      |************************************************** [ 139 ]

Storage Throughput = excellent ( 1552.80 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38575449 bp ( 38575208 non ambiguous )
   - Num Contigs Represented = 203
   - 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.. : 33 raw families identified
   - RepeatScout: Running filtering stage.. 29 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 26 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:46 (hh:mm:ss) Elapsed Time : 23 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...
       233 repeats masked totaling 59740 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10005153 bp
       Num Contigs Represented = 100
       Non ambiguous bp:
             Initial: 10005129 bp
             After Masking: 9931983 bp
             Masked: 0.73 % 
 -- Input Database Coverage: 10005153 bp out of 38575541 bp ( 25.94 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 40755
Comparison Time: 00:03:45 (hh:mm:ss) Elapsed Time, 1829 HSPs Collected
Number of families returned by RECON: 757
Round Time: 00:04:09 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:02 (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...
       640 repeats masked totaling 175704 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28570242 bp
       Num Contigs Represented = 172
       Non ambiguous bp:
             Initial: 28570025 bp
             After Masking: 28349568 bp
             Masked: 0.77 % 
 -- Input Database Coverage: 38575395 bp out of 38575541 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 340725
Comparison Time: 00:14:44 (hh:mm:ss) Elapsed Time, 13847 HSPs Collected
Number of families returned by RECON: 3614
Round Time: 00:15:57 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 34 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.GvM80H/RM_808747.FriSep121957442025
# 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: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:21:00 (hh:mm:ss) Elapsed Time