RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.1IJMuU/RM_14367.MonAug121946572024
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: 1723517216
Database = /dev/shm/rModeler.1IJMuU/GCA_001444555.1_ASM144455v1   - Sequences = 834
  - Bases = 24807186
  - N50 = 115800
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  445408-477187 |                                                   [ 1 ]
  413629-445408 |                                                   [  ]
  381850-413629 |                                                   [  ]
  350071-381850 |                                                   [  ]
  318292-350071 |                                                   [  ]
  286513-318292 |                                                   [ 3 ]
  254734-286513 |                                                   [ 6 ]
  222955-254734 |                                                   [ 3 ]
  191176-222955 |                                                   [ 12 ]
  159397-191176 |*                                                  [ 13 ]
  127618-159397 |*                                                  [ 19 ]
  95839-127618  |*                                                  [ 23 ]
  64060-95839   |***                                                [ 43 ]
  32281-64060   |*****                                              [ 74 ]
  502-32281     |************************************************** [ 637 ]

Storage Throughput = excellent ( 1040.70 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 24807145 bp ( 24807145 non ambiguous )
   - Num Contigs Represented = 834
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:08:15 (hh:mm:ss) Elapsed Time
Round Time: 00:09:14 (hh:mm:ss) Elapsed Time : 84 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 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1754 repeats masked totaling 479909 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10033305 bp
       Num Contigs Represented = 397
       Non ambiguous bp:
             Initial: 10033305 bp
             After Masking: 9539568 bp
             Masked: 4.92 % 
 -- Input Database Coverage: 10033305 bp out of 24807186 bp ( 40.45 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 129795
Comparison Time: 00:05:32 (hh:mm:ss) Elapsed Time, 1832 HSPs Collected
Number of families returned by RECON: 755
Round Time: 00:05:51 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 44807186


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 44807186 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2209 repeats masked totaling 576337 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 14773795 bp
       Num Contigs Represented = 550
       Non ambiguous bp:
             Initial: 14773795 bp
             After Masking: 14173839 bp
             Masked: 4.06 % 
 -- Input Database Coverage: 24807100 bp out of 24807186 bp ( 100.00 % )
Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 272691
Comparison Time: 00:09:41 (hh:mm:ss) Elapsed Time, 4251 HSPs Collected
Number of families returned by RECON: 1277
Round Time: 00:10:15 (hh:mm:ss) Elapsed Time : 3 families discovered.

RepeatScout/RECON discovery complete: 87 families found


Classification Time: 00:02:18 (hh:mm:ss) Elapsed Time


Program Time: 00:27:38 (hh:mm:ss) Elapsed Time