RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.rRvPfq/RM_807980.WedSep101410462025
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: 1757538646
Database = /dev/shm/rModeler.rRvPfq/GCA_018154425.1_ASM1815442v1 
  - Sequences = 425
  - Bases = 19911006
  - N50 = 544601
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1468801-1573702 |                                                   [ 1 ]
  1363901-1468801 |                                                   [  ]
  1259001-1363901 |                                                   [  ]
  1154101-1259001 |                                                   [ 1 ]
  1049201-1154101 |                                                   [  ]
  944301-1049201  |                                                   [ 2 ]
  839401-944301   |                                                   [  ]
  734500-839400   |                                                   [  ]
  629600-734500   |                                                   [ 4 ]
  524700-629600   |                                                   [ 4 ]
  419800-524700   |                                                   [ 3 ]
  314900-419800   |                                                   [ 7 ]
  210000-314900   |*                                                  [ 10 ]
  105100-210000   |*                                                  [ 9 ]
  200-105100      |************************************************** [ 384 ]

Storage Throughput = excellent ( 1658.09 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19910956 bp ( 19517690 non ambiguous )
   - Num Contigs Represented = 425
   - 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.. : 25 raw families identified
   - RepeatScout: Running filtering stage.. 24 families remaining
   - RepeatScout: 00:00:26 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 22 families... 00:00:08 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:00 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:00 (hh:mm:ss) Elapsed Time
Round Time: 00:00:36 (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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       359 repeats masked totaling 64225 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10257910 bp
       Num Contigs Represented = 241
       Non ambiguous bp:
             Initial: 10038008 bp
             After Masking: 9920365 bp
             Masked: 1.17 % 
 -- Input Database Coverage: 10257910 bp out of 19911006 bp ( 51.52 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 100576
Comparison Time: 00:04:54 (hh:mm:ss) Elapsed Time, 19548 HSPs Collected
Number of families returned by RECON: 1687
Round Time: 00:05:28 (hh:mm:ss) Elapsed Time : 5 families discovered.
   - Increasing sample size to include end piece now = 39911006


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39911006 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...
       2771 repeats masked totaling 298018 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9652978 bp
       Num Contigs Represented = 234
       Non ambiguous bp:
             Initial: 9479614 bp
             After Masking: 9129218 bp
             Masked: 3.70 % 
 -- Input Database Coverage: 19910888 bp out of 19911006 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 89253
Comparison Time: 00:04:23 (hh:mm:ss) Elapsed Time, 2173 HSPs Collected
Number of families returned by RECON: 689
Round Time: 00:04:35 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.rRvPfq/RM_807980.WedSep101410462025
# 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: 00:10:45 (hh:mm:ss) Elapsed Time