RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.nApWWU/RM_1407492.FriSep122011202025
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: 1757733080
Database = /dev/shm/rModeler.nApWWU/GCA_051397595.1_GA10_16 
  - Sequences = 247
  - Bases = 38577003
  - N50 = 561328
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1416992-1518170 |                                                   [ 1 ]
  1315814-1416991 |                                                   [ 2 ]
  1214636-1315813 |                                                   [ 2 ]
  1113458-1214635 |                                                   [ 1 ]
  1012280-1113457 |                                                   [  ]
  911102-1012279  |                                                   [ 3 ]
  809924-911101   |                                                   [ 3 ]
  708746-809923   |                                                   [ 1 ]
  607568-708745   |                                                   [ 2 ]
  506390-607567   |**                                                 [ 9 ]
  405212-506389   |***                                                [ 12 ]
  304034-405211   |**                                                 [ 10 ]
  202856-304033   |***                                                [ 13 ]
  101678-202855   |*****                                              [ 20 ]
  501-101678      |************************************************** [ 168 ]

Storage Throughput = excellent ( 1674.36 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38576843 bp ( 38576381 non ambiguous )
   - Num Contigs Represented = 247
   - 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.. : 28 raw families identified
   - RepeatScout: Running filtering stage.. 25 families remaining
   - RepeatScout: 00:00:39 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 23 families... 00:00:10 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:53 (hh:mm:ss) Elapsed Time : 20 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...
       201 repeats masked totaling 59071 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10015139 bp
       Num Contigs Represented = 134
       Non ambiguous bp:
             Initial: 10015027 bp
             After Masking: 9939925 bp
             Masked: 0.75 % 
 -- Input Database Coverage: 10015139 bp out of 38577003 bp ( 25.96 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 45150
Comparison Time: 00:03:47 (hh:mm:ss) Elapsed Time, 1699 HSPs Collected
Number of families returned by RECON: 719
Round Time: 00:04:01 (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 : 00:00:01 (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...
       645 repeats masked totaling 163445 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28561624 bp
       Num Contigs Represented = 196
       Non ambiguous bp:
             Initial: 28561274 bp
             After Masking: 28358105 bp
             Masked: 0.71 % 
 -- Input Database Coverage: 38576763 bp out of 38577003 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 354903
Comparison Time: 00:14:27 (hh:mm:ss) Elapsed Time, 14111 HSPs Collected
Number of families returned by RECON: 3701
Round Time: 00:15:01 (hh:mm:ss) Elapsed Time : 6 families discovered.

RepeatScout/RECON discovery complete: 27 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.nApWWU/RM_1407492.FriSep122011202025
# 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: 00:20:02 (hh:mm:ss) Elapsed Time