RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.K4l4DY/RM_309850.MonSep81339482025
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: 1757363987
Database = /dev/shm/rModeler.K4l4DY/GCA_001466535.1_ASM146653v1 
  - Sequences = 144
  - Bases = 12604920
  - N50 = 318293
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  699726-749632 |*                                                  [ 2 ]
  649821-699726 |                                                   [  ]
  599916-649821 |                                                   [ 1 ]
  550011-599916 |                                                   [  ]
  500106-550011 |                                                   [ 1 ]
  450200-500105 |                                                   [ 1 ]
  400295-450200 |*                                                  [ 2 ]
  350390-400295 |*                                                  [ 3 ]
  300485-350390 |**                                                 [ 4 ]
  250580-300485 |*                                                  [ 3 ]
  200674-250579 |**                                                 [ 4 ]
  150769-200674 |**                                                 [ 5 ]
  100864-150769 |**                                                 [ 5 ]
  50959-100864  |***************                                    [ 27 ]
  1054-50959    |************************************************** [ 86 ]

Storage Throughput = excellent ( 1650.24 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12604814 bp ( 12598627 non ambiguous )
   - Num Contigs Represented = 144
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 20 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:17 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 16 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:23 (hh:mm:ss) Elapsed Time : 12 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 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       212 repeats masked totaling 58329 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10018778 bp
       Num Contigs Represented = 124
       Non ambiguous bp:
             Initial: 10013826 bp
             After Masking: 9894351 bp
             Masked: 1.19 % 
 -- Input Database Coverage: 10018778 bp out of 12604920 bp ( 79.48 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 52003
Comparison Time: 00:04:26 (hh:mm:ss) Elapsed Time, 2745 HSPs Collected
Number of families returned by RECON: 784
Round Time: 00:04:38 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 32604920


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32604920 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       71 repeats masked totaling 12449 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2585956 bp
       Num Contigs Represented = 55
       Non ambiguous bp:
             Initial: 2584721 bp
             After Masking: 2533696 bp
             Masked: 1.97 % 
 -- Input Database Coverage: 12604734 bp out of 12604920 bp ( 100.00 % )
Sampling Time: 00:00:04 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 3741
Comparison Time: 00:00:58 (hh:mm:ss) Elapsed Time, 389 HSPs Collected
Number of families returned by RECON: 98
Round Time: 00:01:02 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 12 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.K4l4DY/RM_309850.MonSep81339482025
# 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: 00:06:09 (hh:mm:ss) Elapsed Time