RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.LkqhDa/RM_4108527.WedFeb110403152026
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: 1770811394
Database = /dev/shm/rModeler.LkqhDa/GCA_030415315.1_ASM3041531v1 
  - Sequences = 196
  - Bases = 9102734
  - N50 = 139010
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  454370-486787 |                                                   [ 1 ]
  421954-454370 |                                                   [ 2 ]
  389538-421954 |                                                   [ 1 ]
  357121-389537 |                                                   [ 1 ]
  324705-357121 |                                                   [  ]
  292289-324705 |                                                   [  ]
  259873-292289 |                                                   [ 1 ]
  227456-259872 |                                                   [ 1 ]
  195040-227456 |*                                                  [ 3 ]
  162624-195040 |                                                   [ 2 ]
  130208-162624 |**                                                 [ 7 ]
  97791-130207  |**                                                 [ 6 ]
  65375-97791   |********                                           [ 21 ]
  32959-65375   |*******                                            [ 19 ]
  543-32959     |************************************************** [ 131 ]

Storage Throughput = excellent ( 1550.56 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 9102635 bp ( 9102184 non ambiguous )
   - Num Contigs Represented = 196
   - 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.. 1 families remaining
   - RepeatScout: 00:00:35 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 1 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 : 1 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...
       14 repeats masked totaling 9385 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9102635 bp
       Num Contigs Represented = 196
       Non ambiguous bp:
             Initial: 9102184 bp
             After Masking: 9020914 bp
             Masked: 0.89 % 
 -- Input Database Coverage: 9102635 bp out of 9102734 bp ( 100.00 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 66430
Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 1102 HSPs Collected
Number of families returned by RECON: 395
Round Time: 00:05:31 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 1 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.LkqhDa/RM_4108527.WedFeb110403152026
# 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: 00:00:04 (hh:mm:ss) Elapsed Time


Program Time: 00:06:15 (hh:mm:ss) Elapsed Time