RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.e3IFoD/RM_839361.FriSep121959442025
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: 1757732383
Database = /dev/shm/rModeler.e3IFoD/GCA_051397495.1_GA15_4 
  - Sequences = 313
  - Bases = 38905770
  - N50 = 350184
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  929795-996173 |                                                   [ 1 ]
  863417-929795 |                                                   [ 2 ]
  797039-863417 |                                                   [  ]
  730661-797039 |                                                   [ 2 ]
  664283-730661 |                                                   [ 3 ]
  597905-664283 |*                                                  [ 4 ]
  531527-597905 |                                                   [ 2 ]
  465149-531527 |**                                                 [ 8 ]
  398771-465149 |*                                                  [ 6 ]
  332393-398771 |**                                                 [ 9 ]
  266015-332393 |***                                                [ 13 ]
  199637-266015 |******                                             [ 22 ]
  133259-199637 |********                                           [ 31 ]
  66881-133259  |*********                                          [ 34 ]
  503-66881     |************************************************** [ 176 ]

Storage Throughput = excellent ( 1541.84 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38905756 bp ( 38905308 non ambiguous )
   - Num Contigs Represented = 313
   - 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.. : 34 raw families identified
   - RepeatScout: Running filtering stage.. 31 families remaining
   - RepeatScout: 00:00:39 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 28 families... 00:00:15 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:58 (hh:mm:ss) Elapsed Time : 24 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...
       199 repeats masked totaling 43878 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10000235 bp
       Num Contigs Represented = 158
       Non ambiguous bp:
             Initial: 10000012 bp
             After Masking: 9937935 bp
             Masked: 0.62 % 
 -- Input Database Coverage: 10000235 bp out of 38905770 bp ( 25.70 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 47586
Comparison Time: 00:03:55 (hh:mm:ss) Elapsed Time, 1861 HSPs Collected
Number of families returned by RECON: 725
Round Time: 00:04:12 (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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       780 repeats masked totaling 212855 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28905501 bp
       Num Contigs Represented = 269
       Non ambiguous bp:
             Initial: 28905276 bp
             After Masking: 28649889 bp
             Masked: 0.88 % 
 -- Input Database Coverage: 38905736 bp out of 38905770 bp ( 100.00 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 385881
Comparison Time: 00:15:21 (hh:mm:ss) Elapsed Time, 13463 HSPs Collected
Number of families returned by RECON: 3629
Round Time: 00:17:20 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 36 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.e3IFoD/RM_839361.FriSep121959442025
# 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: 00:00:10 (hh:mm:ss) Elapsed Time


Program Time: 00:22:40 (hh:mm:ss) Elapsed Time