RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.8vyFxC/RM_12770.TueJun251729052024
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: 1719361745
Database = /dev/shm/rModeler.8vyFxC/GCF_000468235.1_Legionella_pneumophila_Leg01_16   - Sequences = 581
  - Bases = 3658226
  - N50 = 12421
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  45280-48500 |                                                   [ 1 ]
  42060-45280 |                                                   [ 1 ]
  38840-42060 |                                                   [  ]
  35620-38840 |                                                   [ 1 ]
  32400-35620 |                                                   [ 3 ]
  29180-32400 |*                                                  [ 7 ]
  25960-29180 |                                                   [ 2 ]
  22740-25960 |*                                                  [ 9 ]
  19520-22740 |*                                                  [ 9 ]
  16300-19520 |**                                                 [ 15 ]
  13080-16300 |******                                             [ 34 ]
  9860-13080  |*******                                            [ 41 ]
  6640-9860   |*************                                      [ 72 ]
  3420-6640   |************************                           [ 126 ]
  200-3420    |************************************************** [ 260 ]

Storage Throughput = excellent ( 1039.20 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 3658127 bp ( 3658127 non ambiguous )
   - Num Contigs Represented = 581
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:02:31 (hh:mm:ss) Elapsed Time
Round Time: 00:02:41 (hh:mm:ss) Elapsed Time : 5 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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       224 repeats masked totaling 15797 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 3658127 bp
       Num Contigs Represented = 581
       Non ambiguous bp:
             Initial: 3658127 bp
             After Masking: 3640307 bp
             Masked: 0.49 % 
 -- Input Database Coverage: 3658127 bp out of 3658226 bp ( 100.00 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 169653
Comparison Time: 00:02:34 (hh:mm:ss) Elapsed Time, 1260 HSPs Collected
Number of families returned by RECON: 478
Round Time: 00:02:46 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 6 families found


Classification Time: 00:00:03 (hh:mm:ss) Elapsed Time


Program Time: 00:05:30 (hh:mm:ss) Elapsed Time