RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.nw8DtE/RM_728559.FriSep121922112025
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: 1757730131
Database = /dev/shm/rModeler.nw8DtE/GCA_051397275.1_GA10_7 
  - Sequences = 181
  - Bases = 38453877
  - N50 = 835328
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1610847-1725871 |                                                   [ 1 ]
  1495823-1610847 |                                                   [ 1 ]
  1380799-1495823 |                                                   [ 2 ]
  1265775-1380799 |                                                   [  ]
  1150751-1265775 |*                                                  [ 3 ]
  1035727-1150751 |*                                                  [ 3 ]
  920703-1035727  |*                                                  [ 3 ]
  805679-920703   |*                                                  [ 3 ]
  690655-805679   |                                                   [ 1 ]
  575631-690655   |*                                                  [ 4 ]
  460607-575631   |****                                               [ 9 ]
  345583-460607   |****                                               [ 9 ]
  230559-345583   |****                                               [ 11 ]
  115535-230559   |*********                                          [ 20 ]
  511-115535      |*************************************************  [ 111 ]

Storage Throughput = excellent ( 1550.45 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38453776 bp ( 38453482 non ambiguous )
   - Num Contigs Represented = 181
   - 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.. : 22 raw families identified
   - RepeatScout: Running filtering stage.. 20 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 19 families... 00:00:05 (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 : 19 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...
       157 repeats masked totaling 30146 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10017256 bp
       Num Contigs Represented = 97
       Non ambiguous bp:
             Initial: 10017074 bp
             After Masking: 9974359 bp
             Masked: 0.43 % 
 -- Input Database Coverage: 10017256 bp out of 38453877 bp ( 26.05 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 39903
Comparison Time: 00:03:47 (hh:mm:ss) Elapsed Time, 1604 HSPs Collected
Number of families returned by RECON: 750
Round Time: 00:04:00 (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...
       549 repeats masked totaling 130001 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28436440 bp
       Num Contigs Represented = 157
       Non ambiguous bp:
             Initial: 28436328 bp
             After Masking: 28266591 bp
             Masked: 0.60 % 
 -- Input Database Coverage: 38453696 bp out of 38453877 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 323610
Comparison Time: 00:14:30 (hh:mm:ss) Elapsed Time, 14434 HSPs Collected
Number of families returned by RECON: 3654
Round Time: 00:15:06 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 29 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.nw8DtE/RM_728559.FriSep121922112025
# 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