RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.KNOhbc/RM_3523226.FriSep121945532025
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: 1757731552
Database = /data/tmp/rModeler.KNOhbc/GCA_051397415.1_GA10_24 
  - Sequences = 187
  - Bases = 38557102
  - N50 = 866249
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2121604-2273112 |                                                   [ 1 ]
  1970097-2121604 |                                                   [  ]
  1818590-1970097 |                                                   [ 2 ]
  1667083-1818590 |                                                   [ 1 ]
  1515576-1667083 |                                                   [  ]
  1364068-1515575 |                                                   [  ]
  1212561-1364068 |                                                   [ 1 ]
  1061054-1212561 |                                                   [ 2 ]
  909547-1061054  |**                                                 [ 6 ]
  758040-909547   |**                                                 [ 7 ]
  606532-758039   |**                                                 [ 8 ]
  455025-606532   |*                                                  [ 3 ]
  303518-455025   |***                                                [ 9 ]
  152011-303518   |****                                               [ 13 ]
  504-152011      |************************************************** [ 134 ]

Storage Throughput = excellent ( 1544.71 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38557050 bp ( 38556752 non ambiguous )
   - Num Contigs Represented = 187
   - 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.. : 26 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:00:41 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 21 families... 00:00:09 (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: 00:00:55 (hh:mm:ss) Elapsed Time : 18 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       205 repeats masked totaling 55270 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10010146 bp
       Num Contigs Represented = 95
       Non ambiguous bp:
             Initial: 10010077 bp
             After Masking: 9940838 bp
             Masked: 0.69 % 
 -- Input Database Coverage: 10010146 bp out of 38557102 bp ( 25.96 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 43365
Comparison Time: 00:05:02 (hh:mm:ss) Elapsed Time, 1805 HSPs Collected
Number of families returned by RECON: 731
Round Time: 00:05:20 (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 00:00:23 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       579 repeats masked totaling 152917 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28546824 bp
       Num Contigs Represented = 154
       Non ambiguous bp:
             Initial: 28546595 bp
             After Masking: 28352669 bp
             Masked: 0.68 % 
 -- Input Database Coverage: 38556970 bp out of 38557102 bp ( 100.00 % )
Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 326836
Comparison Time: 00:19:05 (hh:mm:ss) Elapsed Time, 13988 HSPs Collected
Number of families returned by RECON: 3610
Round Time: 00:19:59 (hh:mm:ss) Elapsed Time : 7 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.KNOhbc/RM_3523226.FriSep121945532025
# 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: 00:00:10 (hh:mm:ss) Elapsed Time


Program Time: 00:26:24 (hh:mm:ss) Elapsed Time