RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.epgNPj/RM_681837.MonSep81348332025
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: 1757364512
Database = /dev/shm/rModeler.epgNPj/GCA_001466565.1_ASM146656v1 
  - Sequences = 183
  - Bases = 12865870
  - N50 = 225580
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  630361-675315 |                                                   [ 1 ]
  585407-630360 |                                                   [  ]
  540454-585407 |                                                   [  ]
  495500-540453 |                                                   [ 1 ]
  450547-495500 |                                                   [ 1 ]
  405593-450546 |                                                   [ 2 ]
  360639-405592 |                                                   [  ]
  315686-360639 |                                                   [ 2 ]
  270732-315685 |*                                                  [ 4 ]
  225779-270732 |***                                                [ 7 ]
  180825-225778 |*                                                  [ 4 ]
  135871-180824 |***                                                [ 7 ]
  90918-135871  |******                                             [ 15 ]
  45964-90917   |***********                                        [ 26 ]
  1011-45964    |************************************************** [ 113 ]

Storage Throughput = excellent ( 1042.65 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12865786 bp ( 12854914 non ambiguous )
   - Num Contigs Represented = 183
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 21 raw families identified
   - RepeatScout: Running filtering stage.. 17 families remaining
   - RepeatScout: 00:00:42 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 14 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:52 (hh:mm:ss) Elapsed Time : 14 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (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...
       207 repeats masked totaling 42137 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10011539 bp
       Num Contigs Represented = 158
       Non ambiguous bp:
             Initial: 10003492 bp
             After Masking: 9887719 bp
             Masked: 1.16 % 
 -- Input Database Coverage: 10011539 bp out of 12865870 bp ( 77.81 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 58311
Comparison Time: 00:06:56 (hh:mm:ss) Elapsed Time, 3216 HSPs Collected
Number of families returned by RECON: 749
Round Time: 00:07:19 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 32865870


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32865870 bp
   - Sequence extraction : 00:00:01 (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...
       96 repeats masked totaling 20665 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2854180 bp
       Num Contigs Represented = 68
       Non ambiguous bp:
             Initial: 2851355 bp
             After Masking: 2809284 bp
             Masked: 1.48 % 
 -- Input Database Coverage: 12865719 bp out of 12865870 bp ( 100.00 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 4851
Comparison Time: 00:01:19 (hh:mm:ss) Elapsed Time, 234 HSPs Collected
Number of families returned by RECON: 109
Round Time: 00:01:26 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 14 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.epgNPj/RM_681837.MonSep81348332025
# 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: 00:00:12 (hh:mm:ss) Elapsed Time


Program Time: 00:09:49 (hh:mm:ss) Elapsed Time