RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.ZIHzVh/RM_3804256.FriSep121857292025
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: 1757728648
Database = /data/tmp/rModeler.ZIHzVh/GCA_051397115.1_GA10_11 
  - Sequences = 251
  - Bases = 38449598
  - N50 = 515346
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1257006-1346756 |                                                   [ 3 ]
  1167256-1257005 |                                                   [ 1 ]
  1077506-1167255 |                                                   [  ]
  987756-1077505  |                                                   [ 3 ]
  898006-987755   |                                                   [ 1 ]
  808256-898005   |                                                   [  ]
  718506-808255   |*                                                  [ 4 ]
  628756-718505   |                                                   [ 1 ]
  539006-628755   |**                                                 [ 7 ]
  449256-539005   |*                                                  [ 6 ]
  359506-449255   |***                                                [ 11 ]
  269756-359505   |****                                               [ 13 ]
  180006-269755   |*****                                              [ 17 ]
  90256-180005    |********                                           [ 26 ]
  507-90256       |************************************************** [ 158 ]

Storage Throughput = excellent ( 1242.58 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38449457 bp ( 38449114 non ambiguous )
   - Num Contigs Represented = 251
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 23 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:00:42 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 20 families... 00:00:05 (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: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:00:55 (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 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       177 repeats masked totaling 41450 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10024627 bp
       Num Contigs Represented = 119
       Non ambiguous bp:
             Initial: 10024532 bp
             After Masking: 9968464 bp
             Masked: 0.56 % 
 -- Input Database Coverage: 10024627 bp out of 38449598 bp ( 26.07 % )
Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 41041
Comparison Time: 00:04:41 (hh:mm:ss) Elapsed Time, 1846 HSPs Collected
Number of families returned by RECON: 771
Round Time: 00:05:03 (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 00:00:22 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       526 repeats masked totaling 115743 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28424750 bp
       Num Contigs Represented = 223
       Non ambiguous bp:
             Initial: 28424502 bp
             After Masking: 28270583 bp
             Masked: 0.54 % 
 -- Input Database Coverage: 38449377 bp out of 38449598 bp ( 100.00 % )
Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 353220
Comparison Time: 00:18:46 (hh:mm:ss) Elapsed Time, 13579 HSPs Collected
Number of families returned by RECON: 3605
Round Time: 00:19:47 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.ZIHzVh/RM_3804256.FriSep121857292025
# 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: 00:25:55 (hh:mm:ss) Elapsed Time