RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.tMjvNt/RM_302373.WedSep101357592025
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: 1757537879
Database = /dev/shm/rModeler.tMjvNt/GCA_018154095.1_ASM1815409v1 
  - Sequences = 482
  - Bases = 19647002
  - N50 = 394664
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1055564-1130948 |                                                   [ 1 ]
  980181-1055564  |                                                   [  ]
  904798-980181   |                                                   [  ]
  829415-904798   |                                                   [ 1 ]
  754032-829415   |                                                   [  ]
  678648-754031   |                                                   [ 3 ]
  603265-678648   |                                                   [  ]
  527882-603265   |                                                   [ 4 ]
  452499-527882   |                                                   [ 5 ]
  377116-452499   |                                                   [ 2 ]
  301732-377115   |*                                                  [ 11 ]
  226349-301732   |                                                   [ 8 ]
  150966-226349   |*                                                  [ 11 ]
  75583-150966    |*                                                  [ 9 ]
  200-75583       |************************************************** [ 427 ]

Storage Throughput = excellent ( 1673.59 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19646895 bp ( 19643336 non ambiguous )
   - Num Contigs Represented = 482
   - 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.. : 30 raw families identified
   - RepeatScout: Running filtering stage.. 29 families remaining
   - RepeatScout: 00:00:27 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 24 families... 00:00:07 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 5 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:00:38 (hh:mm:ss) Elapsed Time : 19 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       258 repeats masked totaling 46150 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10039297 bp
       Num Contigs Represented = 255
       Non ambiguous bp:
             Initial: 10037207 bp
             After Masking: 9934958 bp
             Masked: 1.02 % 
 -- Input Database Coverage: 10039297 bp out of 19647002 bp ( 51.10 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 102378
Comparison Time: 00:05:00 (hh:mm:ss) Elapsed Time, 20292 HSPs Collected
Number of families returned by RECON: 1555
Round Time: 00:05:37 (hh:mm:ss) Elapsed Time : 10 families discovered.
   - Increasing sample size to include end piece now = 39647002


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39647002 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...
       3206 repeats masked totaling 322326 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9607535 bp
       Num Contigs Represented = 283
       Non ambiguous bp:
             Initial: 9606066 bp
             After Masking: 9227729 bp
             Masked: 3.94 % 
 -- Input Database Coverage: 19646832 bp out of 19647002 bp ( 100.00 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 110685
Comparison Time: 00:04:45 (hh:mm:ss) Elapsed Time, 2934 HSPs Collected
Number of families returned by RECON: 786
Round Time: 00:05:01 (hh:mm:ss) Elapsed Time : 3 families discovered.

RepeatScout/RECON discovery complete: 32 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.tMjvNt/RM_302373.WedSep101357592025
# 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: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:11:23 (hh:mm:ss) Elapsed Time