RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.VYc1F9/RM_1263239.WedFeb112003212026
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: 1770869000
Database = /dev/shm/rModeler.VYc1F9/GCA_004337945.1_UKP13.v0 
  - Sequences = 107
  - Bases = 9030676
  - N50 = 1146512
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1268389-1358970 |                                                   [ 1 ]
  1177809-1268389 |                                                   [ 1 ]
  1087229-1177809 |                                                   [ 1 ]
  996648-1087228  |                                                   [ 1 ]
  906068-996648   |                                                   [  ]
  815488-906068   |*                                                  [ 3 ]
  724908-815488   |                                                   [  ]
  634327-724907   |                                                   [  ]
  543747-634327   |                                                   [ 1 ]
  453167-543747   |                                                   [  ]
  362587-453167   |                                                   [  ]
  272006-362586   |                                                   [ 1 ]
  181426-272006   |                                                   [  ]
  90846-181426    |*                                                  [ 3 ]
  266-90846       |************************************************** [ 95 ]

Storage Throughput = excellent ( 1488.51 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 9030582 bp ( 7154682 non ambiguous )
   - Num Contigs Represented = 107
   - 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: 00:00:13 (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: 00:00:18 (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 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       9 repeats masked totaling 2437 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9030582 bp
       Num Contigs Represented = 107
       Non ambiguous bp:
             Initial: 7154682 bp
             After Masking: 7094140 bp
             Masked: 0.85 % 
 -- Input Database Coverage: 9030582 bp out of 9030676 bp ( 100.00 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 52326
Comparison Time: 00:03:54 (hh:mm:ss) Elapsed Time, 906 HSPs Collected
Number of families returned by RECON: 301
Round Time: 00:04:04 (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.VYc1F9/RM_1263239.WedFeb112003212026
# 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: 00:04:27 (hh:mm:ss) Elapsed Time