RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.W2eHmC/RM_3683636.FriSep122004472025
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: 1757732686
Database = /dev/shm/rModeler.W2eHmC/GCA_051397535.1_GA1_14 
  - Sequences = 263
  - Bases = 38719125
  - N50 = 685312
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1535979-1645656 |                                                   [ 1 ]
  1426302-1535978 |                                                   [  ]
  1316625-1426301 |                                                   [  ]
  1206948-1316624 |                                                   [ 1 ]
  1097271-1206947 |                                                   [ 1 ]
  987594-1097270  |*                                                  [ 6 ]
  877917-987593   |                                                   [ 2 ]
  768240-877916   |                                                   [ 3 ]
  658563-768239   |**                                                 [ 11 ]
  548886-658562   |*                                                  [ 7 ]
  439209-548885   |*                                                  [ 4 ]
  329532-439208   |                                                   [ 3 ]
  219855-329531   |***                                                [ 14 ]
  110178-219854   |*****                                              [ 22 ]
  502-110178      |************************************************** [ 188 ]

Storage Throughput = excellent ( 1688.59 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38719053 bp ( 38718957 non ambiguous )
   - Num Contigs Represented = 263
   - 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.. : 28 raw families identified
   - RepeatScout: Running filtering stage.. 25 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 24 families... 00:00:13 (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: 00:00:54 (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 : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       227 repeats masked totaling 60530 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10033670 bp
       Num Contigs Represented = 124
       Non ambiguous bp:
             Initial: 10033665 bp
             After Masking: 9955278 bp
             Masked: 0.78 % 
 -- Input Database Coverage: 10033670 bp out of 38719125 bp ( 25.91 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 47278
Comparison Time: 00:03:52 (hh:mm:ss) Elapsed Time, 1971 HSPs Collected
Number of families returned by RECON: 790
Round Time: 00:04:08 (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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       768 repeats masked totaling 179002 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28685303 bp
       Num Contigs Represented = 217
       Non ambiguous bp:
             Initial: 28685212 bp
             After Masking: 28464829 bp
             Masked: 0.77 % 
 -- Input Database Coverage: 38718973 bp out of 38719125 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 373680
Comparison Time: 00:14:35 (hh:mm:ss) Elapsed Time, 13289 HSPs Collected
Number of families returned by RECON: 3657
Round Time: 00:15:12 (hh:mm:ss) Elapsed Time : 7 families discovered.

RepeatScout/RECON discovery complete: 32 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.W2eHmC/RM_3683636.FriSep122004472025
# 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: 00:20:21 (hh:mm:ss) Elapsed Time