RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.zp3ZVL/RM_841572.MonSep81351192025
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: 1757364678
Database = /data/tmp/rModeler.zp3ZVL/GCA_001466685.1_ASM146668v1 
  - Sequences = 189
  - Bases = 12820484
  - N50 = 191059
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  647447-693622 |                                                   [ 1 ]
  601272-647446 |                                                   [  ]
  555097-601271 |                                                   [  ]
  508922-555096 |                                                   [  ]
  462748-508922 |*                                                  [ 3 ]
  416573-462747 |                                                   [ 1 ]
  370398-416572 |*                                                  [ 4 ]
  324223-370397 |                                                   [  ]
  278048-324222 |                                                   [ 1 ]
  231874-278048 |                                                   [ 2 ]
  185699-231873 |***                                                [ 8 ]
  139524-185698 |***                                                [ 9 ]
  93349-139523  |*****                                              [ 14 ]
  47174-93348   |***********                                        [ 28 ]
  1000-47174    |************************************************** [ 118 ]

Storage Throughput = excellent ( 1504.26 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12820403 bp ( 12810081 non ambiguous )
   - Num Contigs Represented = 189
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 24 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:00:23 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:05 (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 : 16 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 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       253 repeats masked totaling 59020 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10035748 bp
       Num Contigs Represented = 160
       Non ambiguous bp:
             Initial: 10027820 bp
             After Masking: 9898647 bp
             Masked: 1.29 % 
 -- Input Database Coverage: 10035748 bp out of 12820484 bp ( 78.28 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 62128
Comparison Time: 00:05:22 (hh:mm:ss) Elapsed Time, 2855 HSPs Collected
Number of families returned by RECON: 724
Round Time: 00:05:40 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 32820484


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32820484 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       97 repeats masked totaling 22963 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2784603 bp
       Num Contigs Represented = 75
       Non ambiguous bp:
             Initial: 2782209 bp
             After Masking: 2737240 bp
             Masked: 1.62 % 
 -- Input Database Coverage: 12820351 bp out of 12820484 bp ( 100.00 % )
Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 4465
Comparison Time: 00:01:16 (hh:mm:ss) Elapsed Time, 213 HSPs Collected
Number of families returned by RECON: 97
Round Time: 00:01:22 (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.zp3ZVL/RM_841572.MonSep81351192025
# 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: 00:07:43 (hh:mm:ss) Elapsed Time