RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.3CODjK/RM_6781.MonAug121555062024
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: 1723503305
Database = /dev/shm/rModeler.3CODjK/GCA_000350365.1_Foc4_1.0   - Sequences = 840
  - Bases = 52926277
  - N50 = 2054062
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  5886828-6307302 |                                                   [ 1 ]
  5466355-5886828 |                                                   [  ]
  5045881-5466354 |                                                   [  ]
  4625408-5045881 |                                                   [  ]
  4204934-4625407 |                                                   [ 1 ]
  3784461-4204934 |                                                   [  ]
  3363987-3784460 |                                                   [  ]
  2943514-3363987 |                                                   [  ]
  2523040-2943513 |                                                   [ 2 ]
  2102567-2523040 |                                                   [ 2 ]
  1682093-2102566 |                                                   [ 6 ]
  1261620-1682093 |                                                   [ 3 ]
  841146-1261619  |                                                   [ 5 ]
  420673-841146   |                                                   [ 7 ]
  200-420673      |*************************************************  [ 813 ]

Storage Throughput = good ( 700.69 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 43411828 bp ( 40035543 non ambiguous )
   - Num Contigs Represented = 698
   - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:17:50 (hh:mm:ss) Elapsed Time
Round Time: 00:32:47 (hh:mm:ss) Elapsed Time : 72 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       927 repeats masked totaling 337518 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10848804 bp
       Num Contigs Represented = 210
       Non ambiguous bp:
             Initial: 10012577 bp
             After Masking: 9661602 bp
             Masked: 3.51 % 
 -- Input Database Coverage: 10848804 bp out of 52926277 bp ( 20.50 % )
Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 93961
Comparison Time: 00:05:44 (hh:mm:ss) Elapsed Time, 1430 HSPs Collected
Number of families returned by RECON: 640
Round Time: 00:06:08 (hh:mm:ss) Elapsed Time : 0 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2718 repeats masked totaling 967356 bp(s).
   - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 32562944 bp
       Num Contigs Represented = 532
       Non ambiguous bp:
             Initial: 30022886 bp
             After Masking: 29021404 bp
             Masked: 3.34 % 
 -- Input Database Coverage: 43411748 bp out of 52926277 bp ( 82.02 % )
Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 814726
Comparison Time: 00:30:10 (hh:mm:ss) Elapsed Time, 13576 HSPs Collected
Number of families returned by RECON: 3434
Round Time: 00:31:40 (hh:mm:ss) Elapsed Time : 11 families discovered.
   - Increasing sample size to include end piece now = 102077473


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 102077473 bp
   - Sequence extraction : 00:00:02 (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...
       839 repeats masked totaling 280148 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9514267 bp
       Num Contigs Represented = 184
       Non ambiguous bp:
             Initial: 8772318 bp
             After Masking: 8482643 bp
             Masked: 3.30 % 
 -- Input Database Coverage: 52926015 bp out of 52926277 bp ( 100.00 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 70876
Comparison Time: 00:04:42 (hh:mm:ss) Elapsed Time, 1110 HSPs Collected
Number of families returned by RECON: 529
Round Time: 00:05:01 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 83 families found


Classification Time: 00:05:14 (hh:mm:ss) Elapsed Time


Program Time: 01:20:50 (hh:mm:ss) Elapsed Time