RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.xWGQmq/RM_16981.MonAug121347302024
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: 1723495649
Database = /dev/shm/rModeler.xWGQmq/GCA_000180835.1_ASM18083v1   - Sequences = 41786
  - Bases = 13270809
  - N50 = 442
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  7459-7985 |                                                   [ 1 ]
  6933-7458 |                                                   [  ]
  6408-6933 |                                                   [  ]
  5882-6407 |                                                   [  ]
  5356-5881 |                                                   [ 3 ]
  4831-5356 |                                                   [  ]
  4305-4830 |                                                   [ 2 ]
  3779-4304 |                                                   [ 10 ]
  3254-3779 |                                                   [ 17 ]
  2728-3253 |                                                   [ 42 ]
  2202-2727 |                                                   [ 113 ]
  1677-2202 |                                                   [ 304 ]
  1151-1676 |*                                                  [ 917 ]
  625-1150  |****                                               [ 3212 ]
  100-625   |************************************************** [ 37165 ]

  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 = good ( 916.87 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 13270676 bp ( 13270676 non ambiguous )
   - Num Contigs Represented = 41785
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:10:57 (hh:mm:ss) Elapsed Time
Round Time: 00:12:25 (hh:mm:ss) Elapsed Time : 44 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5640 repeats masked totaling 622145 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10000147 bp
       Num Contigs Represented = 31327
       Non ambiguous bp:
             Initial: 10000147 bp
             After Masking: 9363876 bp
             Masked: 6.36 % 
 -- Input Database Coverage: 10000147 bp out of 13270809 bp ( 75.35 % )
Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 490674801
Comparison Time: 01:48:41 (hh:mm:ss) Elapsed Time, 32931 HSPs Collected
Number of families returned by RECON: 2761
Round Time: 01:52:32 (hh:mm:ss) Elapsed Time : 73 families discovered.
   - Increasing sample size to include end piece now = 33270809


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 33270809 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3143 repeats masked totaling 563415 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 3270528 bp
       Num Contigs Represented = 10458
       Non ambiguous bp:
             Initial: 3270528 bp
             After Masking: 2701576 bp
             Masked: 17.40 % 
 -- Input Database Coverage: 13270675 bp out of 13270809 bp ( 100.00 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 54679653
Comparison Time: 00:32:34 (hh:mm:ss) Elapsed Time, 719 HSPs Collected
Number of families returned by RECON: 397
Round Time: 00:32:53 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 117 families found


Classification Time: 00:04:43 (hh:mm:ss) Elapsed Time


Program Time: 02:42:34 (hh:mm:ss) Elapsed Time