RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.ruEVN5/RM_1832722.ThuSep110623442025
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: 1757597023
Database = /dev/shm/rModeler.ruEVN5/GCA_023628155.1_ASM2362815v1 
  - Sequences = 111
  - Bases = 20661800
  - N50 = 643081
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1601801-1716188 |                                                   [ 1 ]
  1487414-1601800 |                                                   [  ]
  1373027-1487413 |                                                   [  ]
  1258640-1373026 |                                                   [ 1 ]
  1144253-1258639 |                                                   [ 1 ]
  1029866-1144252 |                                                   [ 1 ]
  915479-1029865  |                                                   [  ]
  801092-915478   |*                                                  [ 2 ]
  686705-801091   |**                                                 [ 3 ]
  572318-686704   |***                                                [ 5 ]
  457931-572317   |**                                                 [ 4 ]
  343544-457930   |***                                                [ 5 ]
  229157-343543   |**                                                 [ 4 ]
  114770-229156   |******                                             [ 9 ]
  384-114770      |************************************************** [ 75 ]

Storage Throughput = excellent ( 1615.38 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 20661757 bp ( 20660080 non ambiguous )
   - Num Contigs Represented = 111
   - 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.. : 27 raw families identified
   - RepeatScout: Running filtering stage.. 27 families remaining
   - RepeatScout: 00:00:19 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 27 families... 00:00:07 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 5 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:29 (hh:mm:ss) Elapsed Time : 22 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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       526 repeats masked totaling 131720 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10035628 bp
       Num Contigs Represented = 76
       Non ambiguous bp:
             Initial: 10034946 bp
             After Masking: 9891101 bp
             Masked: 1.43 % 
 -- Input Database Coverage: 10035628 bp out of 20661800 bp ( 48.57 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 42778
Comparison Time: 00:03:56 (hh:mm:ss) Elapsed Time, 1304 HSPs Collected
Number of families returned by RECON: 572
Round Time: 00:04:08 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 40661800


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40661800 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       536 repeats masked totaling 150937 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10626049 bp
       Num Contigs Represented = 76
       Non ambiguous bp:
             Initial: 10625054 bp
             After Masking: 10460555 bp
             Masked: 1.55 % 
 -- Input Database Coverage: 20661677 bp out of 20661800 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 45753
Comparison Time: 00:04:09 (hh:mm:ss) Elapsed Time, 1542 HSPs Collected
Number of families returned by RECON: 616
Round Time: 00:04:17 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 23 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.ruEVN5/RM_1832722.ThuSep110623442025
# 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: 00:09:00 (hh:mm:ss) Elapsed Time