RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.84BLTg/RM_46630.WedFeb110405182026
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: 1770811517
Database = /dev/shm/rModeler.84BLTg/GCA_030415335.1_ASM3041533v1 
  - Sequences = 164
  - Bases = 9108801
  - N50 = 151622
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  578048-619296 |                                                   [ 1 ]
  536801-578048 |                                                   [  ]
  495553-536800 |                                                   [  ]
  454306-495553 |                                                   [ 1 ]
  413059-454306 |                                                   [  ]
  371811-413058 |                                                   [ 1 ]
  330564-371811 |                                                   [ 2 ]
  289316-330563 |                                                   [  ]
  248069-289316 |                                                   [ 1 ]
  206822-248069 |*                                                  [ 4 ]
  165574-206821 |*                                                  [ 4 ]
  124327-165574 |****                                               [ 9 ]
  83079-124326  |*****                                              [ 11 ]
  41832-83079   |*********                                          [ 20 ]
  585-41832     |*************************************************  [ 110 ]

Storage Throughput = excellent ( 1658.30 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 9108747 bp ( 9108292 non ambiguous )
   - Num Contigs Represented = 164
   - 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.. 2 families remaining
   - RepeatScout: 00:00:35 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 2 families... 00:00:02 (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: 00:00:40 (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 : 00:00:01 (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...
       19 repeats masked totaling 11102 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9108747 bp
       Num Contigs Represented = 164
       Non ambiguous bp:
             Initial: 9108292 bp
             After Masking: 9026340 bp
             Masked: 0.90 % 
 -- Input Database Coverage: 9108747 bp out of 9108801 bp ( 100.00 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 56280
Comparison Time: 00:05:16 (hh:mm:ss) Elapsed Time, 1086 HSPs Collected
Number of families returned by RECON: 385
Round Time: 00:05:34 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 2 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.84BLTg/RM_46630.WedFeb110405182026
# 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: 00:06:19 (hh:mm:ss) Elapsed Time