RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.LIVzuM/RM_1149017.WedSep101842142025
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: 1757554934
Database = /data/tmp/rModeler.LIVzuM/GCA_019359935.1_ASM1935993v1 
  - Sequences = 815
  - Bases = 22044533
  - N50 = 66378
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  261532-280177 |                                                   [ 1 ]
  242887-261532 |                                                   [  ]
  224242-242887 |                                                   [ 2 ]
  205597-224242 |                                                   [  ]
  186952-205597 |                                                   [ 2 ]
  168307-186952 |                                                   [ 7 ]
  149662-168307 |                                                   [ 5 ]
  131017-149662 |*                                                  [ 10 ]
  112372-131017 |                                                   [ 8 ]
  93727-112372  |*                                                  [ 15 ]
  75082-93727   |**                                                 [ 27 ]
  56437-75082   |****                                               [ 38 ]
  37792-56437   |********                                           [ 76 ]
  19147-37792   |****************                                   [ 154 ]
  502-19147     |************************************************** [ 470 ]

Storage Throughput = excellent ( 1010.02 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22044431 bp ( 22033496 non ambiguous )
   - Num Contigs Represented = 815
   - 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.. : 6 raw families identified
   - RepeatScout: Running filtering stage.. 6 families remaining
   - RepeatScout: 00:00:32 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 5 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: 00:00:41 (hh:mm:ss) Elapsed Time : 3 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       21 repeats masked totaling 7937 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10021766 bp
       Num Contigs Represented = 419
       Non ambiguous bp:
             Initial: 10016311 bp
             After Masking: 9968343 bp
             Masked: 0.48 % 
 -- Input Database Coverage: 10021766 bp out of 22044533 bp ( 45.46 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 125751
Comparison Time: 00:06:48 (hh:mm:ss) Elapsed Time, 1913 HSPs Collected
Number of families returned by RECON: 626
Round Time: 00:07:11 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 42044533


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42044533 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       92 repeats masked totaling 28605 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 12022606 bp
       Num Contigs Represented = 513
       Non ambiguous bp:
             Initial: 12017126 bp
             After Masking: 11941148 bp
             Masked: 0.63 % 
 -- Input Database Coverage: 22044372 bp out of 22044533 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 186966
Comparison Time: 00:09:32 (hh:mm:ss) Elapsed Time, 2025 HSPs Collected
Number of families returned by RECON: 745
Round Time: 00:10:03 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 8 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.LIVzuM/RM_1149017.WedSep101842142025
# 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: 00:00:10 (hh:mm:ss) Elapsed Time


Program Time: 00:18:05 (hh:mm:ss) Elapsed Time