RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.V8Z6ui/RM_23093.FriAug231622582024
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: 1724455377
Database = /dev/shm/rModeler.V8Z6ui/GCF_000247585.1_PP_INRA-310_V2   - Sequences = 708
  - Bases = 82389172
  - N50 = 897753
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  4409934-4724858 |                                                   [ 1 ]
  4095010-4409933 |                                                   [  ]
  3780086-4095009 |                                                   [  ]
  3465162-3780085 |                                                   [  ]
  3150238-3465161 |                                                   [  ]
  2835314-3150237 |                                                   [ 2 ]
  2520390-2835313 |                                                   [ 1 ]
  2205467-2520390 |                                                   [  ]
  1890543-2205466 |                                                   [ 3 ]
  1575619-1890542 |                                                   [ 3 ]
  1260695-1575618 |                                                   [ 3 ]
  945771-1260694  |                                                   [ 9 ]
  630847-945770   |*                                                  [ 18 ]
  315923-630846   |**                                                 [ 27 ]
  1000-315923     |************************************************** [ 641 ]

Storage Throughput = excellent ( 1148.49 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 61143354 bp ( 40005673 non ambiguous )
   - Num Contigs Represented = 568
   - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:16:22 (hh:mm:ss) Elapsed Time
Round Time: 00:20:13 (hh:mm:ss) Elapsed Time : 468 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:03 (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...
       3684 repeats masked totaling 879293 bp(s).
   - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 15730633 bp
       Num Contigs Represented = 229
       Non ambiguous bp:
             Initial: 10019013 bp
             After Masking: 9131604 bp
             Masked: 8.86 % 
 -- Input Database Coverage: 15730633 bp out of 82389172 bp ( 19.09 % )
Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 123753
Comparison Time: 00:07:21 (hh:mm:ss) Elapsed Time, 7145 HSPs Collected
Number of families returned by RECON: 1876
Round Time: 00:08:08 (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 : 00:00:07 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       11274 repeats masked totaling 2794702 bp(s).
   - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 45452986 bp
       Num Contigs Represented = 462
       Non ambiguous bp:
             Initial: 30013425 bp
             After Masking: 27195731 bp
             Masked: 9.39 % 
 -- Input Database Coverage: 61183619 bp out of 82389172 bp ( 74.26 % )
Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1007490
Comparison Time: 00:39:33 (hh:mm:ss) Elapsed Time, 65537 HSPs Collected
Number of families returned by RECON: 6920
Round Time: 00:43:04 (hh:mm:ss) Elapsed Time : 89 families discovered.
   - Increasing sample size to include end piece now = 126658539


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 126658539 bp
   - Sequence extraction : 00:00:04 (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...
       6018 repeats masked totaling 1551823 bp(s).
   - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 21205378 bp
       Num Contigs Represented = 274
       Non ambiguous bp:
             Initial: 13838742 bp
             After Masking: 12269773 bp
             Masked: 11.34 % 
 -- Input Database Coverage: 82388997 bp out of 82389172 bp ( 100.00 % )
Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 228826
Comparison Time: 00:11:42 (hh:mm:ss) Elapsed Time, 13700 HSPs Collected
Number of families returned by RECON: 2699
Round Time: 00:12:51 (hh:mm:ss) Elapsed Time : 4 families discovered.

RepeatScout/RECON discovery complete: 562 families found


Classification Time: 00:15:41 (hh:mm:ss) Elapsed Time


Program Time: 01:39:57 (hh:mm:ss) Elapsed Time