RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.3MHnKE/RM_9109.MonSep161953072024
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: 1726541586
Database = /dev/shm/rModeler.3MHnKE/GCA_000344925.1_EHA_CB_v1   - Sequences = 1938
  - Bases = 12781904
  - N50 = 8834
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  46851-50057 |                                                   [ 1 ]
  43646-46851 |                                                   [  ]
  40441-43646 |                                                   [ 1 ]
  37236-40441 |                                                   [ 1 ]
  34031-37236 |                                                   [ 3 ]
  30825-34030 |                                                   [ 7 ]
  27620-30825 |                                                   [ 11 ]
  24415-27620 |                                                   [ 8 ]
  21210-24415 |*                                                  [ 24 ]
  18005-21210 |*                                                  [ 33 ]
  14799-18004 |***                                                [ 71 ]
  11594-14799 |****                                               [ 107 ]
  8389-11594  |*********                                          [ 199 ]
  5184-8389   |****************                                   [ 372 ]
  1979-5184   |************************************************** [ 1100 ]

  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 ( 1076.96 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12781764 bp ( 12661740 non ambiguous )
   - Num Contigs Represented = 1938
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:10:38 (hh:mm:ss) Elapsed Time
Round Time: 00:11:09 (hh:mm:ss) Elapsed Time : 14 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 00:00:44 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       459 repeats masked totaling 68048 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10101086 bp
       Num Contigs Represented = 1513
       Non ambiguous bp:
             Initial: 10003334 bp
             After Masking: 9913373 bp
             Masked: 0.90 % 
 -- Input Database Coverage: 10101086 bp out of 12781904 bp ( 79.03 % )
Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1146855
Comparison Time: 00:25:04 (hh:mm:ss) Elapsed Time, 4656 HSPs Collected
Number of families returned by RECON: 976
Round Time: 00:26:28 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 32781904


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32781904 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       181 repeats masked totaling 41784 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2680653 bp
       Num Contigs Represented = 426
       Non ambiguous bp:
             Initial: 2658381 bp
             After Masking: 2611131 bp
             Masked: 1.78 % 
 -- Input Database Coverage: 12781739 bp out of 12781904 bp ( 100.00 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 90525
Comparison Time: 00:03:13 (hh:mm:ss) Elapsed Time, 295 HSPs Collected
Number of families returned by RECON: 142
Round Time: 00:03:30 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 18 families found


Classification Time: 00:00:30 (hh:mm:ss) Elapsed Time


Program Time: 00:41:37 (hh:mm:ss) Elapsed Time