RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.kTHbYq/RM_533116.FriSep121943262025
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: 1757731406
Database = /dev/shm/rModeler.kTHbYq/GCA_051397365.1_GA15_1 
  - Sequences = 242
  - Bases = 38900924
  - N50 = 567022
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1562704-1674290 |                                                   [ 1 ]
  1451118-1562704 |                                                   [  ]
  1339532-1451118 |                                                   [  ]
  1227946-1339532 |                                                   [ 1 ]
  1116360-1227946 |                                                   [ 1 ]
  1004774-1116360 |*                                                  [ 4 ]
  893188-1004774  |                                                   [ 2 ]
  781602-893188   |*                                                  [ 4 ]
  670016-781602   |*                                                  [ 4 ]
  558430-670016   |*                                                  [ 4 ]
  446844-558430   |***                                                [ 10 ]
  335258-446844   |***                                                [ 13 ]
  223672-335258   |***                                                [ 12 ]
  112086-223672   |******                                             [ 20 ]
  500-112086      |************************************************** [ 166 ]

Storage Throughput = excellent ( 1671.62 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38900784 bp ( 38900401 non ambiguous )
   - Num Contigs Represented = 242
   - 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.. : 29 raw families identified
   - RepeatScout: Running filtering stage.. 27 families remaining
   - RepeatScout: 00:00:38 (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), 4 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:00:56 (hh:mm:ss) Elapsed Time : 21 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...
       238 repeats masked totaling 74324 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10017562 bp
       Num Contigs Represented = 127
       Non ambiguous bp:
             Initial: 10017519 bp
             After Masking: 9925232 bp
             Masked: 0.92 % 
 -- Input Database Coverage: 10017562 bp out of 38900924 bp ( 25.75 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 46056
Comparison Time: 00:03:54 (hh:mm:ss) Elapsed Time, 1427 HSPs Collected
Number of families returned by RECON: 684
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...
       826 repeats masked totaling 274305 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28883214 bp
       Num Contigs Represented = 196
       Non ambiguous bp:
             Initial: 28882874 bp
             After Masking: 28567470 bp
             Masked: 1.09 % 
 -- Input Database Coverage: 38900776 bp out of 38900924 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 352380
Comparison Time: 00:14:57 (hh:mm:ss) Elapsed Time, 13702 HSPs Collected
Number of families returned by RECON: 3779
Round Time: 00:15:40 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 32 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.kTHbYq/RM_533116.FriSep121943262025
# 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: 00:00:09 (hh:mm:ss) Elapsed Time


Program Time: 00:20:52 (hh:mm:ss) Elapsed Time