RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.qMTlR3/RM_2020734.ThuDec71709052023
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: 1701997744
Database = /dev/shm/rModeler.qMTlR3/GCA_963082875.1_kaCorEumy4.1   - Sequences = 105
  - Bases = 129324498
  - N50 = 21793380
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  22136153-23716603 |                                                   [ 1 ]
  20555703-22136152 |                                                   [ 1 ]
  18975254-20555703 |                                                   [ 1 ]
  17394804-18975253 |                                                   [ 1 ]
  15814354-17394803 |                                                   [  ]
  14233905-15814354 |*                                                  [ 2 ]
  12653455-14233904 |                                                   [  ]
  11073005-12653454 |                                                   [ 1 ]
  9492556-11073005  |                                                   [  ]
  7912106-9492555   |                                                   [  ]
  6331656-7912105   |                                                   [  ]
  4751207-6331656   |                                                   [  ]
  3170757-4751206   |                                                   [  ]
  1590307-3170756   |                                                   [  ]
  9858-1590307      |************************************************** [ 98 ]

Storage Throughput = good ( 822.76 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40044730 bp ( 40028130 non ambiguous )
   - Num Contigs Represented = 43
   - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:18:43 (hh:mm:ss) Elapsed Time
Round Time: 00:32:16 (hh:mm:ss) Elapsed Time : 307 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6983 repeats masked totaling 1486723 bp(s).
   - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10040575 bp
       Num Contigs Represented = 19
       Non ambiguous bp:
             Initial: 10036575 bp
             After Masking: 7832399 bp
             Masked: 21.96 % 
 -- Input Database Coverage: 10040575 bp out of 129324498 bp ( 7.76 % )
Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33411
Comparison Time: 00:10:14 (hh:mm:ss) Elapsed Time, 46316 HSPs Collected
Number of families returned by RECON: 421
Round Time: 00:12:27 (hh:mm:ss) Elapsed Time : 8 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:04:43 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       23852 repeats masked totaling 5072784 bp(s).
   - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30044075 bp
       Num Contigs Represented = 31
       Non ambiguous bp:
             Initial: 30031475 bp
             After Masking: 22108309 bp
             Masked: 26.38 % 
 -- Input Database Coverage: 40084650 bp out of 129324498 bp ( 31.00 % )
Sampling Time: 00:06:14 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 292995
Comparison Time: 00:53:31 (hh:mm:ss) Elapsed Time, 375691 HSPs Collected
Number of families returned by RECON: 1854
Round Time: 01:01:05 (hh:mm:ss) Elapsed Time : 23 families discovered.


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 90000000 bp
   - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:14:17 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       74593 repeats masked totaling 15450960 bp(s).
   - TE Masking time 00:03:38 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 89239531 bp
       Num Contigs Represented = 71
       Non ambiguous bp:
             Initial: 89207331 bp
             After Masking: 65475239 bp
             Masked: 26.60 % 
 -- Input Database Coverage: 129324181 bp out of 129324498 bp ( 100.00 % )
Sampling Time: 00:18:49 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2582128
Comparison Time: 06:32:15 (hh:mm:ss) Elapsed Time, 1969156 HSPs Collected
Number of families returned by RECON: 7641
Round Time: 06:57:14 (hh:mm:ss) Elapsed Time : 157 families discovered.

RepeatScout/RECON discovery complete: 495 families found


Classification Time: 00:43:50 (hh:mm:ss) Elapsed Time


Program Time: 09:26:52 (hh:mm:ss) Elapsed Time