RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.Jwk3nX/RM_2375361.TueSep90421132025
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: 1757416872
Database = /dev/shm/rModeler.Jwk3nX/GCA_004332445.1_ASM433244v1 
  - Sequences = 158
  - Bases = 12237800
  - N50 = 455037
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1213143-1299761 |                                                   [ 1 ]
  1126526-1213143 |                                                   [  ]
  1039908-1126525 |                                                   [  ]
  953291-1039908  |                                                   [ 1 ]
  866674-953291   |                                                   [  ]
  780056-866673   |                                                   [  ]
  693439-780056   |                                                   [ 1 ]
  606821-693438   |                                                   [ 2 ]
  520204-606821   |                                                   [ 1 ]
  433587-520204   |                                                   [ 2 ]
  346969-433586   |*                                                  [ 4 ]
  260352-346969   |                                                   [ 2 ]
  173734-260351   |***                                                [ 9 ]
  87117-173734    |****                                               [ 12 ]
  500-87117       |************************************************** [ 123 ]

Storage Throughput = excellent ( 1125.37 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12237741 bp ( 12233546 non ambiguous )
   - Num Contigs Represented = 158
   - 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.. : 16 raw families identified
   - RepeatScout: Running filtering stage.. 15 families remaining
   - RepeatScout: 00:00:35 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 14 families... 00:00:07 (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: 00:00:47 (hh:mm:ss) Elapsed Time : 13 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...
       227 repeats masked totaling 64674 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10026345 bp
       Num Contigs Represented = 137
       Non ambiguous bp:
             Initial: 10022608 bp
             After Masking: 9912705 bp
             Masked: 1.10 % 
 -- Input Database Coverage: 10026345 bp out of 12237800 bp ( 81.93 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 62128
Comparison Time: 00:06:57 (hh:mm:ss) Elapsed Time, 3093 HSPs Collected
Number of families returned by RECON: 864
Round Time: 00:07:20 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 32237800


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32237800 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...
       53 repeats masked totaling 12696 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2211316 bp
       Num Contigs Represented = 50
       Non ambiguous bp:
             Initial: 2210858 bp
             After Masking: 2188743 bp
             Masked: 1.00 % 
 -- Input Database Coverage: 12237661 bp out of 12237800 bp ( 100.00 % )
Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 3003
Comparison Time: 00:00:58 (hh:mm:ss) Elapsed Time, 118 HSPs Collected
Number of families returned by RECON: 71
Round Time: 00:01:05 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 13 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.Jwk3nX/RM_2375361.TueSep90421132025
# 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: 00:09:24 (hh:mm:ss) Elapsed Time