RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.0DLW07/RM_1851119.WedSep100734132025
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: 1757514853
Database = /dev/shm/rModeler.0DLW07/GCA_013146005.1_ASM1314600v1 
  - Sequences = 192
  - Bases = 39346150
  - N50 = 729752
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1751901-1877021 |                                                   [ 2 ]
  1626782-1751901 |                                                   [  ]
  1501663-1626782 |                                                   [  ]
  1376543-1501662 |*                                                  [ 4 ]
  1251424-1376543 |                                                   [  ]
  1126305-1251424 |                                                   [  ]
  1001185-1126304 |*                                                  [ 3 ]
  876066-1001185  |                                                   [ 2 ]
  750947-876066   |                                                   [ 2 ]
  625827-750946   |**                                                 [ 7 ]
  500708-625827   |***                                                [ 9 ]
  375589-500708   |***                                                [ 9 ]
  250469-375588   |*****                                              [ 12 ]
  125350-250469   |*********                                          [ 22 ]
  231-125350      |************************************************** [ 120 ]

Storage Throughput = excellent ( 1653.11 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39346012 bp ( 39339940 non ambiguous )
   - Num Contigs Represented = 192
   - 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.. : 35 raw families identified
   - RepeatScout: Running filtering stage.. 21 families remaining
   - RepeatScout: 00:00:47 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 20 families... 00:00:12 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:04 (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 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       176 repeats masked totaling 32696 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10026215 bp
       Num Contigs Represented = 103
       Non ambiguous bp:
             Initial: 10024924 bp
             After Masking: 9974499 bp
             Masked: 0.50 % 
 -- Input Database Coverage: 10026215 bp out of 39346150 bp ( 25.48 % )
Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 42486
Comparison Time: 00:10:38 (hh:mm:ss) Elapsed Time, 1916 HSPs Collected
Number of families returned by RECON: 745
Round Time: 00:10:52 (hh:mm:ss) Elapsed Time : 0 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 00:00:27 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       570 repeats masked totaling 111733 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29319723 bp
       Num Contigs Represented = 163
       Non ambiguous bp:
             Initial: 29314942 bp
             After Masking: 29152681 bp
             Masked: 0.55 % 
 -- Input Database Coverage: 39345938 bp out of 39346150 bp ( 100.00 % )
Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 335790
Comparison Time: 00:51:06 (hh:mm:ss) Elapsed Time, 16786 HSPs Collected
Number of families returned by RECON: 3825
Round Time: 01:14:53 (hh:mm:ss) Elapsed Time : 12 families discovered.

RepeatScout/RECON discovery complete: 31 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.0DLW07/RM_1851119.WedSep100734132025
# 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: 00:00:16 (hh:mm:ss) Elapsed Time


Program Time: 01:27:05 (hh:mm:ss) Elapsed Time