RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.UhjKO4/RM_810100.FriSep121926002025
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: 1757730360
Database = /dev/shm/rModeler.UhjKO4/GCA_051397295.1_GA10_23 
  - Sequences = 163
  - Bases = 38485984
  - N50 = 996771
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1955164-2094783 |                                                   [ 2 ]
  1815546-1955164 |                                                   [  ]
  1675928-1815546 |                                                   [ 1 ]
  1536310-1675928 |                                                   [ 2 ]
  1396692-1536310 |                                                   [ 1 ]
  1257073-1396691 |                                                   [  ]
  1117455-1257073 |                                                   [ 2 ]
  977837-1117455  |***                                                [ 8 ]
  838219-977837   |                                                   [ 1 ]
  698601-838219   |                                                   [ 2 ]
  558982-698600   |**                                                 [ 6 ]
  419364-558982   |***                                                [ 8 ]
  279746-419364   |**                                                 [ 6 ]
  140128-279746   |*******                                            [ 17 ]
  510-140128      |************************************************** [ 107 ]

Storage Throughput = excellent ( 1644.44 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38485841 bp ( 38485439 non ambiguous )
   - Num Contigs Represented = 163
   - 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.. : 23 raw families identified
   - RepeatScout: Running filtering stage.. 21 families remaining
   - RepeatScout: 00:00:38 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:07 (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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       152 repeats masked totaling 46244 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10007511 bp
       Num Contigs Represented = 84
       Non ambiguous bp:
             Initial: 10007402 bp
             After Masking: 9945474 bp
             Masked: 0.62 % 
 -- Input Database Coverage: 10007511 bp out of 38485984 bp ( 26.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 38226
Comparison Time: 00:03:47 (hh:mm:ss) Elapsed Time, 1766 HSPs Collected
Number of families returned by RECON: 764
Round Time: 00:04:01 (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...
       620 repeats masked totaling 158356 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28478250 bp
       Num Contigs Represented = 142
       Non ambiguous bp:
             Initial: 28477957 bp
             After Masking: 28280284 bp
             Masked: 0.69 % 
 -- Input Database Coverage: 38485761 bp out of 38485984 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 317206
Comparison Time: 00:14:18 (hh:mm:ss) Elapsed Time, 13127 HSPs Collected
Number of families returned by RECON: 3491
Round Time: 00:14:51 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 30 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.UhjKO4/RM_810100.FriSep121926002025
# 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: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:19:49 (hh:mm:ss) Elapsed Time