RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.W3tcsO/RM_3782756.FriSep122017152025
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: 1757733435
Database = /dev/shm/rModeler.W3tcsO/GCA_051397615.1_GA8_7 
  - Sequences = 203
  - Bases = 38622354
  - N50 = 606964
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1752617-1877768 |                                                   [ 2 ]
  1627466-1752617 |                                                   [  ]
  1502315-1627466 |                                                   [  ]
  1377164-1502315 |                                                   [ 2 ]
  1252013-1377164 |                                                   [ 2 ]
  1126862-1252013 |                                                   [ 2 ]
  1001711-1126862 |                                                   [  ]
  876560-1001711  |                                                   [ 1 ]
  751409-876560   |*                                                  [ 3 ]
  626258-751409   |*                                                  [ 5 ]
  501107-626258   |**                                                 [ 6 ]
  375956-501107   |****                                               [ 11 ]
  250805-375956   |******                                             [ 17 ]
  125654-250805   |*********                                          [ 24 ]
  503-125654      |************************************************** [ 128 ]

Storage Throughput = excellent ( 1720.51 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38622310 bp ( 38622140 non ambiguous )
   - Num Contigs Represented = 203
   - 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.. : 14 raw families identified
   - RepeatScout: Running filtering stage.. 13 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 11 families... 00:00:04 (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: 00:00:46 (hh:mm:ss) Elapsed Time : 11 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...
       126 repeats masked totaling 18200 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10038436 bp
       Num Contigs Represented = 117
       Non ambiguous bp:
             Initial: 10038365 bp
             After Masking: 9999789 bp
             Masked: 0.38 % 
 -- Input Database Coverage: 10038436 bp out of 38622354 bp ( 25.99 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 45150
Comparison Time: 00:03:52 (hh:mm:ss) Elapsed Time, 2364 HSPs Collected
Number of families returned by RECON: 818
Round Time: 00:04:07 (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...
       396 repeats masked totaling 56967 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28583794 bp
       Num Contigs Represented = 171
       Non ambiguous bp:
             Initial: 28583695 bp
             After Masking: 28483343 bp
             Masked: 0.35 % 
 -- Input Database Coverage: 38622230 bp out of 38622354 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 321201
Comparison Time: 00:14:20 (hh:mm:ss) Elapsed Time, 13233 HSPs Collected
Number of families returned by RECON: 3566
Round Time: 00:14:59 (hh:mm:ss) Elapsed Time : 12 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.W3tcsO/RM_3782756.FriSep122017152025
# 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: 00:19:58 (hh:mm:ss) Elapsed Time