RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.UDeO4e/RM_977629.WedSep101421212025
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: 1757539280
Database = /dev/shm/rModeler.UDeO4e/GCA_018154685.1_ASM1815468v1 
  - Sequences = 366
  - Bases = 19516151
  - N50 = 374703
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1099106-1177600 |                                                   [ 1 ]
  1020613-1099106 |                                                   [ 1 ]
  942120-1020613  |                                                   [ 1 ]
  863626-942119   |                                                   [  ]
  785133-863626   |                                                   [  ]
  706640-785133   |                                                   [  ]
  628146-706639   |                                                   [ 3 ]
  549653-628146   |                                                   [  ]
  471160-549653   |                                                   [ 3 ]
  392666-471159   |                                                   [ 5 ]
  314173-392666   |*                                                  [ 8 ]
  235680-314173   |*                                                  [ 10 ]
  157186-235679   |*                                                  [ 11 ]
  78693-157186    |**                                                 [ 15 ]
  200-78693       |************************************************** [ 308 ]

Storage Throughput = excellent ( 1656.66 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19516081 bp ( 19506720 non ambiguous )
   - Num Contigs Represented = 366
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 19 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:27 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 19 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:34 (hh:mm:ss) Elapsed Time : 17 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       378 repeats masked totaling 58795 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10010773 bp
       Num Contigs Represented = 222
       Non ambiguous bp:
             Initial: 10005673 bp
             After Masking: 9893691 bp
             Masked: 1.12 % 
 -- Input Database Coverage: 10010773 bp out of 19516151 bp ( 51.29 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 88410
Comparison Time: 00:04:45 (hh:mm:ss) Elapsed Time, 17567 HSPs Collected
Number of families returned by RECON: 1538
Round Time: 00:05:18 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 39516151


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39516151 bp
   - Sequence extraction : 00:00:00 (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...
       2692 repeats masked totaling 246867 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9505228 bp
       Num Contigs Represented = 202
       Non ambiguous bp:
             Initial: 9500967 bp
             After Masking: 9200051 bp
             Masked: 3.17 % 
 -- Input Database Coverage: 19516001 bp out of 19516151 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 74691
Comparison Time: 00:04:18 (hh:mm:ss) Elapsed Time, 2389 HSPs Collected
Number of families returned by RECON: 784
Round Time: 00:04:34 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 21 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.UDeO4e/RM_977629.WedSep101421212025
# 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: 00:10:32 (hh:mm:ss) Elapsed Time