RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.d5v7g2/RM_3490250.FriSep121954582025
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: 1757732098
Database = /dev/shm/rModeler.d5v7g2/GCA_051397455.1_GA10_8 
  - Sequences = 197
  - Bases = 38421897
  - N50 = 678839
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2084084-2232912 |                                                   [ 1 ]
  1935257-2084084 |                                                   [ 1 ]
  1786430-1935257 |                                                   [  ]
  1637603-1786430 |                                                   [  ]
  1488776-1637603 |                                                   [ 2 ]
  1339949-1488776 |                                                   [ 2 ]
  1191122-1339949 |                                                   [ 1 ]
  1042294-1191121 |                                                   [ 2 ]
  893467-1042294  |*                                                  [ 3 ]
  744640-893467   |                                                   [ 1 ]
  595813-744640   |**                                                 [ 7 ]
  446986-595813   |**                                                 [ 8 ]
  298159-446986   |****                                               [ 12 ]
  149332-298159   |******                                             [ 19 ]
  505-149332      |************************************************** [ 138 ]

Storage Throughput = excellent ( 1737.11 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38421815 bp ( 38421628 non ambiguous )
   - Num Contigs Represented = 197
   - 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.. : 20 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:38 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 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: 00:00:47 (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 : 00:00:00 (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...
       175 repeats masked totaling 33047 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10004852 bp
       Num Contigs Represented = 92
       Non ambiguous bp:
             Initial: 10004793 bp
             After Masking: 9959215 bp
             Masked: 0.46 % 
 -- Input Database Coverage: 10004852 bp out of 38421897 bp ( 26.04 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 39903
Comparison Time: 00:03:45 (hh:mm:ss) Elapsed Time, 1653 HSPs Collected
Number of families returned by RECON: 739
Round Time: 00:03:58 (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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       582 repeats masked totaling 92342 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28416935 bp
       Num Contigs Represented = 172
       Non ambiguous bp:
             Initial: 28416807 bp
             After Masking: 28283423 bp
             Masked: 0.47 % 
 -- Input Database Coverage: 38421787 bp out of 38421897 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 334153
Comparison Time: 00:14:03 (hh:mm:ss) Elapsed Time, 13297 HSPs Collected
Number of families returned by RECON: 3546
Round Time: 00:14:45 (hh:mm:ss) Elapsed Time : 12 families discovered.

RepeatScout/RECON discovery complete: 32 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.d5v7g2/RM_3490250.FriSep121954582025
# 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: 00:19:37 (hh:mm:ss) Elapsed Time