RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.hRvf0b/RM_1381051.FriSep122032452025
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: 1757734365
Database = /dev/shm/rModeler.hRvf0b/GCA_051397675.1_GA10_10 
  - Sequences = 202
  - Bases = 38508758
  - N50 = 607360
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1825512-1955871 |                                                   [ 1 ]
  1695154-1825512 |                                                   [  ]
  1564796-1695154 |                                                   [  ]
  1434438-1564796 |                                                   [ 1 ]
  1304080-1434438 |                                                   [  ]
  1173722-1304080 |                                                   [ 1 ]
  1043364-1173722 |                                                   [ 2 ]
  913006-1043364  |*                                                  [ 3 ]
  782648-913006   |*                                                  [ 3 ]
  652290-782648   |**                                                 [ 7 ]
  521932-652290   |***                                                [ 9 ]
  391574-521932   |****                                               [ 11 ]
  261216-391574   |******                                             [ 16 ]
  130858-261216   |******                                             [ 16 ]
  500-130858      |************************************************** [ 132 ]

Storage Throughput = excellent ( 1686.99 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38508691 bp ( 38508375 non ambiguous )
   - Num Contigs Represented = 202
   - 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: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:08 (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: 00:00:49 (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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       175 repeats masked totaling 46085 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10023197 bp
       Num Contigs Represented = 103
       Non ambiguous bp:
             Initial: 10023008 bp
             After Masking: 9960337 bp
             Masked: 0.63 % 
 -- Input Database Coverage: 10023197 bp out of 38508758 bp ( 26.03 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 41041
Comparison Time: 00:04:02 (hh:mm:ss) Elapsed Time, 1693 HSPs Collected
Number of families returned by RECON: 706
Round Time: 00:04:14 (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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       594 repeats masked totaling 152207 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28485414 bp
       Num Contigs Represented = 174
       Non ambiguous bp:
             Initial: 28485287 bp
             After Masking: 28294797 bp
             Masked: 0.67 % 
 -- Input Database Coverage: 38508611 bp out of 38508758 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 332520
Comparison Time: 00:14:47 (hh:mm:ss) Elapsed Time, 13567 HSPs Collected
Number of families returned by RECON: 3656
Round Time: 00:15:22 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.hRvf0b/RM_1381051.FriSep122032452025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:20:31 (hh:mm:ss) Elapsed Time