RepeatModeler Version 2.0.4
===========================
Using output directory = /scratch/tmp/rModeler.lFWVZh/RM_3732233.WedDec40912202024
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: 1733332339
Database = /scratch/tmp/rModeler.lFWVZh/GCA_030386735.1_Fv_Alternosema1   - Sequences = 611
  - Bases = 1517482
  - N50 = 2803
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  19732-21070 |                                                   [ 1 ]
  18394-19732 |                                                   [  ]
  17056-18394 |                                                   [  ]
  15718-17056 |                                                   [  ]
  14380-15718 |                                                   [  ]
  13042-14380 |                                                   [  ]
  11704-13042 |                                                   [  ]
  10366-11704 |                                                   [ 1 ]
  9028-10366  |                                                   [ 2 ]
  7690-9028   |                                                   [ 4 ]
  6352-7690   |                                                   [ 7 ]
  5014-6352   |**                                                 [ 19 ]
  3676-5014   |*******                                            [ 54 ]
  2338-3676   |**********************                             [ 161 ]
  1000-2338   |************************************************** [ 362 ]

  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 ( 1498.79 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 1517425 bp ( 1517425 non ambiguous )
   - Num Contigs Represented = 611
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:00:14 (hh:mm:ss) Elapsed Time
Round Time: 00:00:18 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       50 repeats masked totaling 6422 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 1517425 bp
       Num Contigs Represented = 611
       Non ambiguous bp:
             Initial: 1517425 bp
             After Masking: 1507189 bp
             Masked: 0.67 % 
 -- Input Database Coverage: 1517425 bp out of 1517482 bp ( 100.00 % )
Sampling Time: 00:00:02 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 186355
Comparison Time: 00:01:32 (hh:mm:ss) Elapsed Time, 501 HSPs Collected
Number of families returned by RECON: 127
Round Time: 00:01:37 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 2 families found


Classification Time: 00:00:02 (hh:mm:ss) Elapsed Time


Program Time: 00:01:57 (hh:mm:ss) Elapsed Time