RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.s7n7xG/RM_15120.TueSep92324182025
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: 1757485457
Database = /data/tmp/rModeler.s7n7xG/GCA_012922885.1_R265_cen10delta_Chr10-7 
  - Sequences = 122
  - Bases = 17419212
  - N50 = 394047
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  856640-917792 |*                                                  [ 2 ]
  795488-856639 |                                                   [  ]
  734337-795488 |                                                   [  ]
  673185-734336 |*                                                  [ 2 ]
  612034-673185 |                                                   [ 1 ]
  550882-612033 |**                                                 [ 3 ]
  489731-550882 |**                                                 [ 3 ]
  428579-489730 |*                                                  [ 2 ]
  367428-428579 |                                                   [ 1 ]
  306276-367427 |****                                               [ 6 ]
  245125-306276 |****                                               [ 5 ]
  183973-245124 |*****                                              [ 7 ]
  122822-183973 |**********                                         [ 13 ]
  61670-122821  |************                                       [ 15 ]
  519-61670     |************************************************** [ 62 ]

Storage Throughput = excellent ( 1520.73 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 17419151 bp ( 17418919 non ambiguous )
   - Num Contigs Represented = 122
   - 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.. : 19 raw families identified
   - RepeatScout: Running filtering stage.. 17 families remaining
   - RepeatScout: 00:00:16 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 17 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 5 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:25 (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 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       171 repeats masked totaling 31588 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10007343 bp
       Num Contigs Represented = 88
       Non ambiguous bp:
             Initial: 10007230 bp
             After Masking: 9963616 bp
             Masked: 0.44 % 
 -- Input Database Coverage: 10007343 bp out of 17419212 bp ( 57.45 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 42486
Comparison Time: 00:04:49 (hh:mm:ss) Elapsed Time, 3016 HSPs Collected
Number of families returned by RECON: 648
Round Time: 00:05:09 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 37419212


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 37419212 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       245 repeats masked totaling 48103 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 7411765 bp
       Num Contigs Represented = 86
       Non ambiguous bp:
             Initial: 7411646 bp
             After Masking: 7355260 bp
             Masked: 0.76 % 
 -- Input Database Coverage: 17419108 bp out of 17419212 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 24753
Comparison Time: 00:03:33 (hh:mm:ss) Elapsed Time, 886 HSPs Collected
Number of families returned by RECON: 341
Round Time: 00:03:42 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 16 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.s7n7xG/RM_15120.TueSep92324182025
# 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: 00:00:09 (hh:mm:ss) Elapsed Time


Program Time: 00:09:25 (hh:mm:ss) Elapsed Time