RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.CelCyW/RM_3059015.ThuFeb120006272026
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: 1770883586
Database = /dev/shm/rModeler.CelCyW/GCA_002093605.1_ASM209360v1 
  - Sequences = 309
  - Bases = 9082089
  - N50 = 77027
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  216903-232359 |                                                   [ 3 ]
  201447-216902 |                                                   [  ]
  185991-201446 |                                                   [  ]
  170535-185990 |                                                   [  ]
  155080-170535 |                                                   [ 1 ]
  139624-155079 |                                                   [ 3 ]
  124168-139623 |**                                                 [ 10 ]
  108712-124167 |*                                                  [ 6 ]
  93256-108711  |*                                                  [ 4 ]
  77801-93256   |**                                                 [ 9 ]
  62345-77800   |****                                               [ 16 ]
  46889-62344   |****                                               [ 17 ]
  31433-46888   |********                                           [ 29 ]
  15977-31432   |**********                                         [ 38 ]
  522-15977     |************************************************** [ 173 ]

Storage Throughput = excellent ( 1665.17 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 9082000 bp ( 9081695 non ambiguous )
   - Num Contigs Represented = 309
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 3 raw families identified
   - RepeatScout: Running filtering stage.. 3 families remaining
   - RepeatScout: 00:00:35 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 3 families... 00:00:04 (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: 00:00:41 (hh:mm:ss) Elapsed Time : 2 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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       34 repeats masked totaling 8841 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9082000 bp
       Num Contigs Represented = 309
       Non ambiguous bp:
             Initial: 9081695 bp
             After Masking: 9002839 bp
             Masked: 0.87 % 
 -- Input Database Coverage: 9082000 bp out of 9082089 bp ( 100.00 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 99681
Comparison Time: 00:05:39 (hh:mm:ss) Elapsed Time, 1386 HSPs Collected
Number of families returned by RECON: 528
Round Time: 00:06:01 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 3 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.CelCyW/RM_3059015.ThuFeb120006272026
# 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: 00:00:05 (hh:mm:ss) Elapsed Time


Program Time: 00:06:47 (hh:mm:ss) Elapsed Time