RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.bpnZ9f/RM_4073209.FriSep121910142025
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: 1757729413
Database = /dev/shm/rModeler.bpnZ9f/GCA_051397185.1_GA8_2 
  - Sequences = 191
  - Bases = 38648802
  - N50 = 752580
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1950600-2089892 |                                                   [ 1 ]
  1811308-1950599 |                                                   [ 1 ]
  1672016-1811307 |                                                   [ 2 ]
  1532725-1672016 |                                                   [ 1 ]
  1393433-1532724 |                                                   [  ]
  1254141-1393432 |                                                   [ 2 ]
  1114849-1254140 |                                                   [ 1 ]
  975558-1114849  |                                                   [ 1 ]
  836266-975557   |*                                                  [ 4 ]
  696974-836265   |*                                                  [ 3 ]
  557682-696973   |*                                                  [ 5 ]
  418391-557682   |*****                                              [ 16 ]
  279099-418390   |****                                               [ 11 ]
  139807-279098   |**                                                 [ 7 ]
  516-139807      |*************************************************  [ 136 ]

Storage Throughput = excellent ( 1633.34 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38648659 bp ( 38648338 non ambiguous )
   - Num Contigs Represented = 191
   - 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.. : 13 raw families identified
   - RepeatScout: Running filtering stage.. 12 families remaining
   - RepeatScout: 00:00:38 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 11 families... 00:00:04 (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: 00:00:46 (hh:mm:ss) Elapsed Time : 11 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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       103 repeats masked totaling 15673 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10011575 bp
       Num Contigs Represented = 88
       Non ambiguous bp:
             Initial: 10011539 bp
             After Masking: 9980609 bp
             Masked: 0.31 % 
 -- Input Database Coverage: 10011575 bp out of 38648802 bp ( 25.90 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 37950
Comparison Time: 00:03:44 (hh:mm:ss) Elapsed Time, 2131 HSPs Collected
Number of families returned by RECON: 780
Round Time: 00:03:58 (hh:mm:ss) Elapsed Time : 4 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 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...
       516 repeats masked totaling 74175 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28637007 bp
       Num Contigs Represented = 165
       Non ambiguous bp:
             Initial: 28636722 bp
             After Masking: 28513783 bp
             Masked: 0.43 % 
 -- Input Database Coverage: 38648582 bp out of 38648802 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 339900
Comparison Time: 00:15:04 (hh:mm:ss) Elapsed Time, 13417 HSPs Collected
Number of families returned by RECON: 3699
Round Time: 00:15:38 (hh:mm:ss) Elapsed Time : 13 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.bpnZ9f/RM_4073209.FriSep121910142025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:20:28 (hh:mm:ss) Elapsed Time