RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.f0d6Tr/RM_667086.MonSep81852572025
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: 1757382776
Database = /dev/shm/rModeler.f0d6Tr/GCA_002572885.1_Emmon_parv_130 
  - Sequences = 383
  - Bases = 27837035
  - N50 = 174248
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  669299-717034 |                                                   [ 1 ]
  621564-669298 |                                                   [  ]
  573829-621563 |                                                   [  ]
  526094-573828 |                                                   [ 1 ]
  478359-526093 |                                                   [ 1 ]
  430624-478358 |                                                   [ 2 ]
  382889-430623 |                                                   [ 3 ]
  335155-382889 |                                                   [ 2 ]
  287420-335154 |                                                   [ 4 ]
  239685-287419 |*                                                  [ 6 ]
  191950-239684 |****                                               [ 21 ]
  144215-191949 |******                                             [ 29 ]
  96480-144214  |*******                                            [ 33 ]
  48745-96479   |*************                                      [ 60 ]
  1011-48745    |*************************************************  [ 220 ]

Storage Throughput = excellent ( 1660.27 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 27836957 bp ( 27832697 non ambiguous )
   - Num Contigs Represented = 383
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 19 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:33 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 19 families... 00:01:02 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:38 (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 : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       193 repeats masked totaling 218357 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10022082 bp
       Num Contigs Represented = 219
       Non ambiguous bp:
             Initial: 10021417 bp
             After Masking: 9779912 bp
             Masked: 2.41 % 
 -- Input Database Coverage: 10022082 bp out of 27837035 bp ( 36.00 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 58996
Comparison Time: 00:04:19 (hh:mm:ss) Elapsed Time, 1256 HSPs Collected
Number of families returned by RECON: 447
Round Time: 00:04:37 (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 : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       468 repeats masked totaling 443808 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 17814795 bp
       Num Contigs Represented = 294
       Non ambiguous bp:
             Initial: 17811200 bp
             After Masking: 17326277 bp
             Masked: 2.72 % 
 -- Input Database Coverage: 27836877 bp out of 27837035 bp ( 100.00 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 182106
Comparison Time: 00:08:43 (hh:mm:ss) Elapsed Time, 2274 HSPs Collected
Number of families returned by RECON: 962
Round Time: 00:09:07 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 17 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.f0d6Tr/RM_667086.MonSep81852572025
# 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: 00:15:32 (hh:mm:ss) Elapsed Time