RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.csdBLZ/RM_7866.TueAug130212002024
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: 1723540319
Database = /dev/shm/rModeler.csdBLZ/GCA_004325045.1_FIOER33_v1   - Sequences = 2915
  - Bases = 18344352
  - N50 = 9589
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  56282-60231 |                                                   [ 2 ]
  52333-56281 |                                                   [ 3 ]
  48384-52332 |                                                   [ 2 ]
  44436-48384 |                                                   [  ]
  40487-44435 |                                                   [ 6 ]
  36538-40486 |                                                   [ 6 ]
  32589-36537 |                                                   [ 10 ]
  28641-32589 |                                                   [ 9 ]
  24692-28640 |                                                   [ 20 ]
  20743-24691 |*                                                  [ 35 ]
  16794-20742 |**                                                 [ 90 ]
  12846-16794 |****                                               [ 149 ]
  8897-12845  |********                                           [ 287 ]
  4948-8896   |*******************                                [ 639 ]
  1000-4948   |************************************************** [ 1657 ]

  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 = excellent ( 1054.92 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18344261 bp ( 18344261 non ambiguous )
   - Num Contigs Represented = 2915
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:10:29 (hh:mm:ss) Elapsed Time
Round Time: 00:14:27 (hh:mm:ss) Elapsed Time : 110 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 00:00:43 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       7094 repeats masked totaling 1900052 bp(s).
   - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10002159 bp
       Num Contigs Represented = 1598
       Non ambiguous bp:
             Initial: 10002159 bp
             After Masking: 7929053 bp
             Masked: 20.73 % 
 -- Input Database Coverage: 10002159 bp out of 18344352 bp ( 54.52 % )
Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1282401
Comparison Time: 00:18:27 (hh:mm:ss) Elapsed Time, 18422 HSPs Collected
Number of families returned by RECON: 1025
Round Time: 00:20:10 (hh:mm:ss) Elapsed Time : 18 families discovered.
   - Increasing sample size to include end piece now = 38344352


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38344352 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6723 repeats masked totaling 2025043 bp(s).
   - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8342090 bp
       Num Contigs Represented = 1322
       Non ambiguous bp:
             Initial: 8342090 bp
             After Masking: 6185851 bp
             Masked: 25.85 % 
 -- Input Database Coverage: 18344249 bp out of 18344352 bp ( 100.00 % )
Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 878475
Comparison Time: 00:13:21 (hh:mm:ss) Elapsed Time, 2588 HSPs Collected
Number of families returned by RECON: 678
Round Time: 00:14:24 (hh:mm:ss) Elapsed Time : 3 families discovered.

RepeatScout/RECON discovery complete: 131 families found


Classification Time: 00:05:37 (hh:mm:ss) Elapsed Time


Program Time: 00:54:38 (hh:mm:ss) Elapsed Time