RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.aXWGOi/RM_18653.TueAug130237592024
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: 1723541878
Database = /dev/shm/rModeler.aXWGOi/GCA_004325075.1_ILG3_v1   - Sequences = 2738
  - Bases = 25202660
  - N50 = 12460
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  78469-84002 |                                                   [ 1 ]
  72936-78468 |                                                   [ 2 ]
  67403-72935 |                                                   [ 3 ]
  61870-67402 |                                                   [ 4 ]
  56337-61869 |                                                   [ 1 ]
  50804-56336 |                                                   [ 6 ]
  45271-50803 |                                                   [ 6 ]
  39738-45270 |                                                   [ 10 ]
  34205-39737 |                                                   [ 15 ]
  28672-34204 |*                                                  [ 35 ]
  23139-28671 |**                                                 [ 65 ]
  17606-23138 |*****                                              [ 150 ]
  12073-17605 |*************                                      [ 345 ]
  6540-12072  |*******************************                    [ 814 ]
  1008-6540   |************************************************** [ 1281 ]

Storage Throughput = excellent ( 1039.36 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 25202600 bp ( 25202600 non ambiguous )
   - Num Contigs Represented = 2738
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:14:12 (hh:mm:ss) Elapsed Time
Round Time: 00:31:20 (hh:mm:ss) Elapsed Time : 218 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 00:00:42 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       8115 repeats masked totaling 3102223 bp(s).
   - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10004621 bp
       Num Contigs Represented = 1065
       Non ambiguous bp:
             Initial: 10004621 bp
             After Masking: 6750394 bp
             Masked: 32.53 % 
 -- Input Database Coverage: 10004621 bp out of 25202660 bp ( 39.70 % )
Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 570846
Comparison Time: 00:14:40 (hh:mm:ss) Elapsed Time, 2512 HSPs Collected
Number of families returned by RECON: 839
Round Time: 00:16:13 (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 00:01:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       12716 repeats masked totaling 4987059 bp(s).
   - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 15197933 bp
       Num Contigs Represented = 1689
       Non ambiguous bp:
             Initial: 15197933 bp
             After Masking: 9933895 bp
             Masked: 34.64 % 
 -- Input Database Coverage: 25202554 bp out of 25202660 bp ( 100.00 % )
Sampling Time: 00:01:53 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1444150
Comparison Time: 00:28:12 (hh:mm:ss) Elapsed Time, 6563 HSPs Collected
Number of families returned by RECON: 1702
Round Time: 00:30:40 (hh:mm:ss) Elapsed Time : 4 families discovered.

RepeatScout/RECON discovery complete: 223 families found


Classification Time: 00:12:55 (hh:mm:ss) Elapsed Time


Program Time: 01:31:08 (hh:mm:ss) Elapsed Time