RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.CVbmXV/RM_2668527.FriSep122229122025
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: 1757741352
Database = /dev/shm/rModeler.CVbmXV/GCA_051943715.1_ASM5194371v1 
  - Sequences = 1510
  - Bases = 22555953
  - N50 = 48138
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  243362-260731 |                                                   [ 1 ]
  225993-243361 |                                                   [  ]
  208624-225992 |                                                   [  ]
  191256-208624 |                                                   [  ]
  173887-191255 |                                                   [ 1 ]
  156518-173886 |                                                   [ 2 ]
  139149-156517 |                                                   [ 6 ]
  121781-139149 |                                                   [ 5 ]
  104412-121780 |                                                   [ 12 ]
  87043-104411  |                                                   [ 12 ]
  69674-87042   |*                                                  [ 29 ]
  52306-69674   |**                                                 [ 57 ]
  34937-52305   |****                                               [ 103 ]
  17568-34936   |*******                                            [ 176 ]
  200-17568     |************************************************** [ 1106 ]

Storage Throughput = excellent ( 1662.72 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22555840 bp ( 22554721 non ambiguous )
   - Num Contigs Represented = 1510
   - Sequence extraction : 00:00:01 (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.. 22 families remaining
   - RepeatScout: 00:00:24 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 22 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:31 (hh:mm:ss) Elapsed Time : 20 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       252 repeats masked totaling 66445 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10015289 bp
       Num Contigs Represented = 751
       Non ambiguous bp:
             Initial: 10014852 bp
             After Masking: 9911261 bp
             Masked: 1.03 % 
 -- Input Database Coverage: 10015289 bp out of 22555953 bp ( 44.40 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 332520
Comparison Time: 00:05:31 (hh:mm:ss) Elapsed Time, 1673 HSPs Collected
Number of families returned by RECON: 656
Round Time: 00:05:55 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 42555953


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42555953 bp
   - Sequence extraction : 00:00:00 (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...
       348 repeats masked totaling 105276 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 12540533 bp
       Num Contigs Represented = 865
       Non ambiguous bp:
             Initial: 12539851 bp
             After Masking: 12386160 bp
             Masked: 1.23 % 
 -- Input Database Coverage: 22555822 bp out of 22555953 bp ( 100.00 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 457446
Comparison Time: 00:07:13 (hh:mm:ss) Elapsed Time, 2485 HSPs Collected
Number of families returned by RECON: 978
Round Time: 00:07:28 (hh:mm:ss) Elapsed Time : 3 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.CVbmXV/RM_2668527.FriSep122229122025
# 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: 00:14:00 (hh:mm:ss) Elapsed Time