RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.VTWXwS/RM_3411532.FriSep121919162025
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: 1757729955
Database = /dev/shm/rModeler.VTWXwS/GCA_051397255.1_GA10_3 
  - Sequences = 233
  - Bases = 38431240
  - N50 = 470864
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1602436-1716860 |                                                   [ 1 ]
  1488012-1602436 |                                                   [  ]
  1373588-1488012 |                                                   [  ]
  1259164-1373588 |                                                   [  ]
  1144740-1259164 |                                                   [ 1 ]
  1030316-1144740 |                                                   [ 2 ]
  915892-1030316  |                                                   [ 1 ]
  801468-915892   |*                                                  [ 3 ]
  687044-801468   |                                                   [ 2 ]
  572620-687044   |**                                                 [ 7 ]
  458196-572620   |***                                                [ 9 ]
  343772-458196   |****                                               [ 12 ]
  229348-343772   |*********                                          [ 28 ]
  114924-229348   |******                                             [ 20 ]
  500-114924      |************************************************** [ 147 ]

Storage Throughput = excellent ( 1610.26 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38431185 bp ( 38430589 non ambiguous )
   - Num Contigs Represented = 233
   - 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.. : 21 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:36 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 16 families... 00:00:05 (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: 00:00:45 (hh:mm:ss) Elapsed Time : 16 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...
       153 repeats masked totaling 23699 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10041198 bp
       Num Contigs Represented = 129
       Non ambiguous bp:
             Initial: 10041032 bp
             After Masking: 10003229 bp
             Masked: 0.38 % 
 -- Input Database Coverage: 10041198 bp out of 38431240 bp ( 26.13 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 42486
Comparison Time: 00:03:48 (hh:mm:ss) Elapsed Time, 2050 HSPs Collected
Number of families returned by RECON: 781
Round Time: 00:04:04 (hh:mm:ss) Elapsed Time : 4 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       621 repeats masked totaling 94111 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28389923 bp
       Num Contigs Represented = 196
       Non ambiguous bp:
             Initial: 28389493 bp
             After Masking: 28255037 bp
             Masked: 0.47 % 
 -- Input Database Coverage: 38431121 bp out of 38431240 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 337431
Comparison Time: 00:14:28 (hh:mm:ss) Elapsed Time, 12514 HSPs Collected
Number of families returned by RECON: 3526
Round Time: 00:15:09 (hh:mm:ss) Elapsed Time : 5 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.VTWXwS/RM_3411532.FriSep121919162025
# 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: 00:20:05 (hh:mm:ss) Elapsed Time