RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.HeZl0I/RM_1286260.FriSep121914272025
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: 1757729667
Database = /data/tmp/rModeler.HeZl0I/GCA_051397235.1_GA10_12 
  - Sequences = 238
  - Bases = 38425112
  - N50 = 537871
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1230464-1318319 |*                                                  [ 3 ]
  1142609-1230463 |                                                   [  ]
  1054755-1142609 |                                                   [ 1 ]
  966900-1054754  |                                                   [  ]
  879046-966900   |                                                   [ 1 ]
  791191-879045   |                                                   [ 2 ]
  703336-791190   |*                                                  [ 5 ]
  615482-703336   |**                                                 [ 6 ]
  527627-615481   |**                                                 [ 7 ]
  439773-527627   |*                                                  [ 4 ]
  351918-439772   |***                                                [ 9 ]
  264063-351917   |*******                                            [ 21 ]
  176209-264063   |****                                               [ 13 ]
  88354-176208    |*******                                            [ 22 ]
  500-88354       |************************************************** [ 144 ]

Storage Throughput = good ( 942.62 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38425032 bp ( 38424809 non ambiguous )
   - Num Contigs Represented = 238
   - 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.. : 22 raw families identified
   - RepeatScout: Running filtering stage.. 21 families remaining
   - RepeatScout: 00:00:40 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 19 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: 00:00:50 (hh:mm:ss) Elapsed Time : 19 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 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       159 repeats masked totaling 29145 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10024133 bp
       Num Contigs Represented = 133
       Non ambiguous bp:
             Initial: 10024097 bp
             After Masking: 9980684 bp
             Masked: 0.43 % 
 -- Input Database Coverage: 10024133 bp out of 38425112 bp ( 26.09 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 43071
Comparison Time: 00:04:26 (hh:mm:ss) Elapsed Time, 1828 HSPs Collected
Number of families returned by RECON: 745
Round Time: 00:04:46 (hh:mm:ss) Elapsed Time : 3 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 00:00:20 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       653 repeats masked totaling 102776 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28400819 bp
       Num Contigs Represented = 199
       Non ambiguous bp:
             Initial: 28400632 bp
             After Masking: 28258880 bp
             Masked: 0.50 % 
 -- Input Database Coverage: 38424952 bp out of 38425112 bp ( 100.00 % )
Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 354061
Comparison Time: 00:18:37 (hh:mm:ss) Elapsed Time, 13012 HSPs Collected
Number of families returned by RECON: 3604
Round Time: 00:19:24 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 30 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.HeZl0I/RM_1286260.FriSep121914272025
# 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: 00:00:09 (hh:mm:ss) Elapsed Time


Program Time: 00:25:09 (hh:mm:ss) Elapsed Time