RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.5iX3vd/RM_1084508.ThuSep111445002025
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: 1757627099
Database = /dev/shm/rModeler.5iX3vd/GCA_025767625.1_ASM2576762v1 
  - Sequences = 691
  - Bases = 14908300
  - N50 = 83678
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  545541-584473 |                                                   [ 1 ]
  506609-545540 |                                                   [  ]
  467678-506609 |                                                   [ 2 ]
  428746-467677 |                                                   [  ]
  389815-428746 |                                                   [ 1 ]
  350883-389814 |                                                   [  ]
  311952-350883 |                                                   [ 1 ]
  273020-311951 |                                                   [ 3 ]
  234089-273020 |                                                   [ 1 ]
  195157-234088 |                                                   [ 4 ]
  156226-195157 |                                                   [ 1 ]
  117294-156225 |*                                                  [ 12 ]
  78363-117294  |*                                                  [ 16 ]
  39431-78362   |****                                               [ 53 ]
  500-39431     |************************************************** [ 596 ]

Storage Throughput = excellent ( 1604.78 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14908277 bp ( 14605038 non ambiguous )
   - Num Contigs Represented = 691
   - 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.. : 23 raw families identified
   - RepeatScout: Running filtering stage.. 23 families remaining
   - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 21 families... 00:00:11 (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: 00:01:17 (hh:mm:ss) Elapsed Time : 20 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       370 repeats masked totaling 155120 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10187934 bp
       Num Contigs Represented = 507
       Non ambiguous bp:
             Initial: 10000323 bp
             After Masking: 9762284 bp
             Masked: 2.38 % 
 -- Input Database Coverage: 10187934 bp out of 14908300 bp ( 68.34 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 206403
Comparison Time: 00:07:07 (hh:mm:ss) Elapsed Time, 6013 HSPs Collected
Number of families returned by RECON: 1268
Round Time: 00:07:34 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 34908300


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34908300 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       184 repeats masked totaling 57420 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4720314 bp
       Num Contigs Represented = 239
       Non ambiguous bp:
             Initial: 4604686 bp
             After Masking: 4513284 bp
             Masked: 1.98 % 
 -- Input Database Coverage: 14908248 bp out of 14908300 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 37128
Comparison Time: 00:02:34 (hh:mm:ss) Elapsed Time, 821 HSPs Collected
Number of families returned by RECON: 329
Round Time: 00:02:52 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 23 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.5iX3vd/RM_1084508.ThuSep111445002025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:11:49 (hh:mm:ss) Elapsed Time