RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.HTTQxX/RM_1102187.FriSep121906592025
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: 1757729219
Database = /data/tmp/rModeler.HTTQxX/GCA_051397155.1_GA10_14 
  - Sequences = 197
  - Bases = 38594460
  - N50 = 1047665
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2468387-2644665 |                                                   [ 2 ]
  2292110-2468387 |                                                   [  ]
  2115833-2292110 |                                                   [  ]
  1939556-2115833 |                                                   [ 2 ]
  1763279-1939556 |                                                   [  ]
  1587001-1763278 |                                                   [  ]
  1410724-1587001 |*                                                  [ 4 ]
  1234447-1410724 |                                                   [ 1 ]
  1058170-1234447 |                                                   [ 1 ]
  881893-1058170  |*                                                  [ 6 ]
  705615-881892   |*                                                  [ 4 ]
  529338-705615   |**                                                 [ 8 ]
  353061-529338   |*                                                  [ 4 ]
  176784-353061   |****                                               [ 13 ]
  507-176784      |************************************************** [ 152 ]

Storage Throughput = good ( 944.76 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38594370 bp ( 38594244 non ambiguous )
   - Num Contigs Represented = 197
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 31 raw families identified
   - RepeatScout: Running filtering stage.. 26 families remaining
   - RepeatScout: 00:01:01 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 23 families... 00:00:17 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 6 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:29 (hh:mm:ss) Elapsed Time : 17 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 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       187 repeats masked totaling 49186 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10020040 bp
       Num Contigs Represented = 89
       Non ambiguous bp:
             Initial: 10019940 bp
             After Masking: 9956260 bp
             Masked: 0.64 % 
 -- Input Database Coverage: 10020040 bp out of 38594460 bp ( 25.96 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 42195
Comparison Time: 00:06:07 (hh:mm:ss) Elapsed Time, 1725 HSPs Collected
Number of families returned by RECON: 726
Round Time: 00:06:45 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       558 repeats masked totaling 149079 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28574319 bp
       Num Contigs Represented = 159
       Non ambiguous bp:
             Initial: 28574293 bp
             After Masking: 28381916 bp
             Masked: 0.67 % 
 -- Input Database Coverage: 38594359 bp out of 38594460 bp ( 100.00 % )
Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 347361
Comparison Time: 00:26:37 (hh:mm:ss) Elapsed Time, 14699 HSPs Collected
Number of families returned by RECON: 3645
Round Time: 00:29:40 (hh:mm:ss) Elapsed Time : 7 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.HTTQxX/RM_1102187.FriSep121906592025
# 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: 00:00:20 (hh:mm:ss) Elapsed Time


Program Time: 00:38:14 (hh:mm:ss) Elapsed Time