RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.gwjrmo/RM_29819.MonSep161947282024
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: 1726541247
Database = /dev/shm/rModeler.gwjrmo/GCA_000365475.1_EHA_CA_v1   - Sequences = 1685
  - Bases = 12292336
  - N50 = 9683
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  84096-90019 |                                                   [ 1 ]
  78173-84095 |                                                   [  ]
  72250-78172 |                                                   [  ]
  66328-72250 |                                                   [  ]
  60405-66327 |                                                   [  ]
  54482-60404 |                                                   [ 1 ]
  48559-54481 |                                                   [  ]
  42637-48559 |                                                   [ 2 ]
  36714-42636 |                                                   [ 2 ]
  30791-36713 |                                                   [ 12 ]
  24868-30790 |*                                                  [ 24 ]
  18946-24868 |**                                                 [ 49 ]
  13023-18945 |******                                             [ 131 ]
  7100-13022  |*****************                                  [ 374 ]
  1178-7100   |************************************************** [ 1089 ]

  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 ( 1086.15 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12292282 bp ( 12285355 non ambiguous )
   - Num Contigs Represented = 1685
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:10:36 (hh:mm:ss) Elapsed Time
Round Time: 00:11:26 (hh:mm:ss) Elapsed Time : 18 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 00:00:48 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       623 repeats masked totaling 107306 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10013889 bp
       Num Contigs Represented = 1370
       Non ambiguous bp:
             Initial: 10006962 bp
             After Masking: 9873954 bp
             Masked: 1.33 % 
 -- Input Database Coverage: 10013889 bp out of 12292336 bp ( 81.46 % )
Sampling Time: 00:00:54 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 940506
Comparison Time: 00:28:09 (hh:mm:ss) Elapsed Time, 5629 HSPs Collected
Number of families returned by RECON: 1053
Round Time: 00:29:50 (hh:mm:ss) Elapsed Time : 5 families discovered.
   - Increasing sample size to include end piece now = 32292336


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32292336 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       230 repeats masked totaling 51691 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2278380 bp
       Num Contigs Represented = 318
       Non ambiguous bp:
             Initial: 2278380 bp
             After Masking: 2221257 bp
             Masked: 2.51 % 
 -- Input Database Coverage: 12292269 bp out of 12292336 bp ( 100.00 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 50403
Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 146 HSPs Collected
Number of families returned by RECON: 97
Round Time: 00:03:09 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 23 families found


Classification Time: 00:00:59 (hh:mm:ss) Elapsed Time


Program Time: 00:45:24 (hh:mm:ss) Elapsed Time