RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.mdhAIi/RM_1036406.WedSep101438282025
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: 1757540307
Database = /data/tmp/rModeler.mdhAIi/GCA_018154945.1_ASM1815494v1 
  - Sequences = 1538
  - Bases = 21059893
  - N50 = 319011
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1506434-1614023 |                                                   [ 1 ]
  1398846-1506434 |                                                   [  ]
  1291258-1398846 |                                                   [  ]
  1183670-1291258 |                                                   [  ]
  1076082-1183670 |                                                   [  ]
  968493-1076081  |                                                   [ 1 ]
  860905-968493   |                                                   [ 1 ]
  753317-860905   |                                                   [ 1 ]
  645729-753317   |                                                   [  ]
  538141-645729   |                                                   [ 2 ]
  430552-538140   |                                                   [ 4 ]
  322964-430552   |                                                   [ 6 ]
  215376-322964   |                                                   [ 12 ]
  107788-215376   |                                                   [ 21 ]
  200-107788      |************************************************** [ 1489 ]

Storage Throughput = excellent ( 1707.69 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 21059784 bp ( 19961958 non ambiguous )
   - Num Contigs Represented = 1538
   - 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.. : 32 raw families identified
   - RepeatScout: Running filtering stage.. 32 families remaining
   - RepeatScout: 00:00:32 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 29 families... 00:00:05 (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: 00:00:40 (hh:mm:ss) Elapsed Time : 27 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 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       474 repeats masked totaling 73892 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10431117 bp
       Num Contigs Represented = 852
       Non ambiguous bp:
             Initial: 10022051 bp
             After Masking: 9889286 bp
             Masked: 1.32 % 
 -- Input Database Coverage: 10431117 bp out of 21059893 bp ( 49.53 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 534061
Comparison Time: 00:07:31 (hh:mm:ss) Elapsed Time, 18246 HSPs Collected
Number of families returned by RECON: 1742
Round Time: 00:08:10 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 41059893


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 41059893 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2550 repeats masked totaling 280620 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10628602 bp
       Num Contigs Represented = 748
       Non ambiguous bp:
             Initial: 9939842 bp
             After Masking: 9604948 bp
             Masked: 3.37 % 
 -- Input Database Coverage: 21059719 bp out of 21059893 bp ( 100.00 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 426426
Comparison Time: 00:06:43 (hh:mm:ss) Elapsed Time, 3196 HSPs Collected
Number of families returned by RECON: 1011
Round Time: 00:07:03 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 32 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.mdhAIi/RM_1036406.WedSep101438282025
# 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: 00:00:09 (hh:mm:ss) Elapsed Time


Program Time: 00:16:02 (hh:mm:ss) Elapsed Time