RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.RfsmFc/RM_214571.FriSep121855422025
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: 1757728541
Database = /dev/shm/rModeler.RfsmFc/GCA_051397075.1_GA11_16 
  - Sequences = 219
  - Bases = 38646405
  - N50 = 653755
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1461638-1566005 |                                                   [ 1 ]
  1357271-1461637 |                                                   [ 1 ]
  1252904-1357270 |                                                   [ 1 ]
  1148537-1252903 |                                                   [ 2 ]
  1044171-1148537 |                                                   [ 1 ]
  939804-1044170  |*                                                  [ 4 ]
  835437-939803   |                                                   [ 2 ]
  731070-835436   |*                                                  [ 3 ]
  626703-731069   |*                                                  [ 5 ]
  522337-626703   |***                                                [ 9 ]
  417970-522336   |**                                                 [ 7 ]
  313603-417969   |**                                                 [ 7 ]
  209236-313602   |****                                               [ 13 ]
  104869-209235   |******                                             [ 19 ]
  503-104869      |************************************************** [ 144 ]

Storage Throughput = excellent ( 1564.44 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38646248 bp ( 38645653 non ambiguous )
   - Num Contigs Represented = 219
   - 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.. 27 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 25 families... 00:00:12 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 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 : 23 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...
       228 repeats masked totaling 50641 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10015288 bp
       Num Contigs Represented = 110
       Non ambiguous bp:
             Initial: 10015072 bp
             After Masking: 9946344 bp
             Masked: 0.69 % 
 -- Input Database Coverage: 10015288 bp out of 38646405 bp ( 25.92 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 41616
Comparison Time: 00:03:50 (hh:mm:ss) Elapsed Time, 1884 HSPs Collected
Number of families returned by RECON: 788
Round Time: 00:04:04 (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 : 00:00:02 (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...
       691 repeats masked totaling 193500 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28630911 bp
       Num Contigs Represented = 186
       Non ambiguous bp:
             Initial: 28630532 bp
             After Masking: 28396841 bp
             Masked: 0.82 % 
 -- Input Database Coverage: 38646199 bp out of 38646405 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 348195
Comparison Time: 00:14:49 (hh:mm:ss) Elapsed Time, 13045 HSPs Collected
Number of families returned by RECON: 3567
Round Time: 00:15:39 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 36 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.RfsmFc/RM_214571.FriSep121855422025
# 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: 00:20:43 (hh:mm:ss) Elapsed Time