RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.XgwbBi/RM_3336.TueAug130358452024
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: 1723546724
Database = /dev/shm/rModeler.XgwbBi/GCA_009176385.1_Asppar1   - Sequences = 270
  - Bases = 38390758
  - N50 = 355580
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1151058-1233205 |                                                   [ 1 ]
  1068911-1151057 |                                                   [ 1 ]
  986764-1068910  |                                                   [  ]
  904617-986763   |                                                   [ 1 ]
  822470-904616   |                                                   [ 1 ]
  740323-822469   |                                                   [  ]
  658176-740322   |*                                                  [ 3 ]
  576029-658175   |**                                                 [ 8 ]
  493882-576028   |*                                                  [ 3 ]
  411735-493881   |***                                                [ 9 ]
  329588-411734   |***                                                [ 9 ]
  247441-329587   |****                                               [ 14 ]
  165294-247440   |**********                                         [ 30 ]
  83147-165293    |*************                                      [ 41 ]
  1001-83147      |************************************************** [ 149 ]

Storage Throughput = excellent ( 1033.19 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38390637 bp ( 38384238 non ambiguous )
   - Num Contigs Represented = 270
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:14:38 (hh:mm:ss) Elapsed Time
Round Time: 00:20:19 (hh:mm:ss) Elapsed Time : 34 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...
       238 repeats masked totaling 47496 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10011221 bp
       Num Contigs Represented = 136
       Non ambiguous bp:
             Initial: 10009683 bp
             After Masking: 9951102 bp
             Masked: 0.59 % 
 -- Input Database Coverage: 10011221 bp out of 38390758 bp ( 26.08 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 40470
Comparison Time: 00:04:37 (hh:mm:ss) Elapsed Time, 1459 HSPs Collected
Number of families returned by RECON: 701
Round Time: 00:04:56 (hh:mm:ss) Elapsed Time : 0 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       774 repeats masked totaling 162409 bp(s).
   - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28379340 bp
       Num Contigs Represented = 249
       Non ambiguous bp:
             Initial: 28374479 bp
             After Masking: 28174295 bp
             Masked: 0.71 % 
 -- Input Database Coverage: 38390561 bp out of 38390758 bp ( 100.00 % )
Sampling Time: 00:00:44 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 355746
Comparison Time: 00:24:12 (hh:mm:ss) Elapsed Time, 12302 HSPs Collected
Number of families returned by RECON: 3524
Round Time: 00:30:40 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 44 families found


Classification Time: 00:02:32 (hh:mm:ss) Elapsed Time


Program Time: 00:58:27 (hh:mm:ss) Elapsed Time