RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.WE4nD8/RM_14168.WedAug141209052024
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: 1723662544
Database = /dev/shm/rModeler.WE4nD8/GCA_001299535.1_ASM129953v1   - Sequences = 1216
  - Bases = 27764161
  - N50 = 72023
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  305070-326845 |                                                   [ 1 ]
  283296-305070 |                                                   [ 1 ]
  261522-283296 |                                                   [ 3 ]
  239748-261522 |                                                   [  ]
  217974-239748 |                                                   [ 3 ]
  196199-217973 |                                                   [ 1 ]
  174425-196199 |                                                   [ 3 ]
  152651-174425 |                                                   [ 4 ]
  130877-152651 |                                                   [ 14 ]
  109103-130877 |                                                   [ 16 ]
  87328-109102  |*                                                  [ 30 ]
  65554-87328   |***                                                [ 63 ]
  43780-65554   |*****                                              [ 88 ]
  22006-43780   |*******                                            [ 129 ]
  232-22006     |************************************************** [ 860 ]

Storage Throughput = excellent ( 1045.23 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 27764089 bp ( 27601190 non ambiguous )
   - Num Contigs Represented = 1216
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:13:02 (hh:mm:ss) Elapsed Time
Round Time: 00:13:28 (hh:mm:ss) Elapsed Time : 4 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       49 repeats masked totaling 6806 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10076888 bp
       Num Contigs Represented = 504
       Non ambiguous bp:
             Initial: 10015267 bp
             After Masking: 9982328 bp
             Masked: 0.33 % 
 -- Input Database Coverage: 10076888 bp out of 27764161 bp ( 36.29 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 170820
Comparison Time: 00:07:21 (hh:mm:ss) Elapsed Time, 1596 HSPs Collected
Number of families returned by RECON: 640
Round Time: 00:07:46 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       225 repeats masked totaling 21108 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 17687159 bp
       Num Contigs Represented = 845
       Non ambiguous bp:
             Initial: 17585881 bp
             After Masking: 17517139 bp
             Masked: 0.39 % 
 -- Input Database Coverage: 27764047 bp out of 27764161 bp ( 100.00 % )
Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 541320
Comparison Time: 00:17:17 (hh:mm:ss) Elapsed Time, 4337 HSPs Collected
Number of families returned by RECON: 1557
Round Time: 00:18:06 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 7 families found


Classification Time: 00:00:13 (hh:mm:ss) Elapsed Time


Program Time: 00:39:33 (hh:mm:ss) Elapsed Time