RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.5y2xsj/RM_9909.TueAug130254132024
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: 1723542853
Database = /dev/shm/rModeler.5y2xsj/GCA_004919615.1_Ncer_3.0   - Sequences = 110
  - Bases = 8816425
  - N50 = 195769
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  561304-600794 |                                                   [ 1 ]
  521814-561303 |                                                   [  ]
  482324-521813 |                                                   [  ]
  442834-482323 |                                                   [ 1 ]
  403344-442833 |                                                   [ 1 ]
  363854-403343 |                                                   [ 1 ]
  324364-363853 |                                                   [  ]
  284874-324363 |***                                                [ 5 ]
  245384-284873 |                                                   [  ]
  205894-245383 |**                                                 [ 3 ]
  166404-205893 |**                                                 [ 3 ]
  126914-166403 |***                                                [ 4 ]
  87424-126913  |*******                                            [ 10 ]
  47934-87423   |************                                       [ 16 ]
  8445-47934    |************************************************** [ 65 ]

Storage Throughput = excellent ( 1052.42 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 8816308 bp ( 8816308 non ambiguous )
   - Num Contigs Represented = 110
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:02:51 (hh:mm:ss) Elapsed Time
Round Time: 00:10:51 (hh:mm:ss) Elapsed Time : 152 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 00:00:36 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6013 repeats masked totaling 3632550 bp(s).
   - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8816308 bp
       Num Contigs Represented = 110
       Non ambiguous bp:
             Initial: 8816308 bp
             After Masking: 5143259 bp
             Masked: 41.66 % 
 -- Input Database Coverage: 8816308 bp out of 8816425 bp ( 100.00 % )
Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 37675
Comparison Time: 00:07:52 (hh:mm:ss) Elapsed Time, 5903 HSPs Collected
Number of families returned by RECON: 736
Round Time: 00:09:38 (hh:mm:ss) Elapsed Time : 5 families discovered.

RepeatScout/RECON discovery complete: 157 families found


Classification Time: 00:28:00 (hh:mm:ss) Elapsed Time


Program Time: 00:48:29 (hh:mm:ss) Elapsed Time