RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.95LsEU/RM_2533985.FriSep120130462025
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: 1757665845
Database = /dev/shm/rModeler.95LsEU/GCA_030563865.1_ASM3056386v1 
  - Sequences = 147
  - Bases = 14047882
  - N50 = 312755
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  834177-893725 |                                                   [ 1 ]
  774629-834176 |                                                   [  ]
  715082-774629 |                                                   [ 1 ]
  655534-715081 |                                                   [  ]
  595986-655533 |                                                   [ 1 ]
  536439-595986 |                                                   [ 1 ]
  476891-536438 |*                                                  [ 2 ]
  417343-476890 |*                                                  [ 3 ]
  357796-417343 |*                                                  [ 2 ]
  298248-357795 |*                                                  [ 3 ]
  238700-298247 |****                                               [ 9 ]
  179153-238700 |*                                                  [ 3 ]
  119605-179152 |*******                                            [ 14 ]
  60057-119604  |******                                             [ 13 ]
  510-60057     |************************************************** [ 94 ]

Storage Throughput = excellent ( 1689.03 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14047805 bp ( 14041705 non ambiguous )
   - Num Contigs Represented = 147
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 13 raw families identified
   - RepeatScout: Running filtering stage.. 9 families remaining
   - RepeatScout: 00:00:20 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 7 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: 00:00:27 (hh:mm:ss) Elapsed Time : 7 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 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       120 repeats masked totaling 31884 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10010825 bp
       Num Contigs Represented = 119
       Non ambiguous bp:
             Initial: 10006425 bp
             After Masking: 9859583 bp
             Masked: 1.47 % 
 -- Input Database Coverage: 10010825 bp out of 14047882 bp ( 71.26 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 51681
Comparison Time: 00:05:24 (hh:mm:ss) Elapsed Time, 4186 HSPs Collected
Number of families returned by RECON: 815
Round Time: 00:05:43 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 34047882


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34047882 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...
       104 repeats masked totaling 20408 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4036944 bp
       Num Contigs Represented = 70
       Non ambiguous bp:
             Initial: 4035244 bp
             After Masking: 3964487 bp
             Masked: 1.75 % 
 -- Input Database Coverage: 14047769 bp out of 14047882 bp ( 100.00 % )
Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 8515
Comparison Time: 00:01:47 (hh:mm:ss) Elapsed Time, 682 HSPs Collected
Number of families returned by RECON: 188
Round Time: 00:01:54 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 10 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.95LsEU/RM_2533985.FriSep120130462025
# 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: 00:00:05 (hh:mm:ss) Elapsed Time


Program Time: 00:08:09 (hh:mm:ss) Elapsed Time