RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.YTIaLF/RM_21067.MonAug121352002024
Search Engine = rmblast 2.13.0+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1723495919
Database = /dev/shm/rModeler.YTIaLF/GCA_000182985.1_ASM18298v1   - Sequences = 5465
  - Bases = 7860219
  - N50 = 2902
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  61266-65607 |                                                   [ 1 ]
  56926-61266 |                                                   [ 1 ]
  52585-56925 |                                                   [  ]
  48245-52585 |                                                   [  ]
  43904-48244 |                                                   [ 1 ]
  39564-43904 |                                                   [  ]
  35223-39563 |                                                   [ 3 ]
  30883-35223 |                                                   [  ]
  26542-30882 |                                                   [ 5 ]
  22202-26542 |                                                   [ 8 ]
  17861-22201 |                                                   [ 22 ]
  13521-17861 |                                                   [ 29 ]
  9180-13520  |                                                   [ 66 ]
  4840-9180   |*                                                  [ 163 ]
  500-4840    |************************************************** [ 5166 ]

  WARN: The N50 for this assembly is low ( <10,000 ).  The de novo methods
        employed by RepeatModeler are intended for use with long contiguous
        sequences and may not perform well with an over-abundance of short
        contigs in the database.
Storage Throughput = excellent ( 1035.73 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 7860163 bp ( 7860163 non ambiguous )
   - Num Contigs Represented = 5465
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:02:52 (hh:mm:ss) Elapsed Time
Round Time: 00:06:21 (hh:mm:ss) Elapsed Time : 246 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 00:00:32 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       9509 repeats masked totaling 2553177 bp(s).
   - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 7860163 bp
       Num Contigs Represented = 5465
       Non ambiguous bp:
             Initial: 7860163 bp
             After Masking: 5265478 bp
             Masked: 33.01 % 
 -- Input Database Coverage: 7860163 bp out of 7860219 bp ( 100.00 % )
Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 14946778
Comparison Time: 00:22:44 (hh:mm:ss) Elapsed Time, 21245 HSPs Collected
Number of families returned by RECON: 1852
Round Time: 00:24:15 (hh:mm:ss) Elapsed Time : 48 families discovered.

RepeatScout/RECON discovery complete: 294 families found


Classification Time: 00:13:41 (hh:mm:ss) Elapsed Time


Program Time: 00:44:17 (hh:mm:ss) Elapsed Time