RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.BU7R6R/RM_27449.TueAug131445202024
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: 1723585518
Database = /dev/shm/rModeler.BU7R6R/GCA_024516155.1_Pyrom1   - Sequences = 260
  - Bases = 61002793
  - N50 = 713190
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1785046-1912478 |                                                   [ 1 ]
  1657614-1785045 |                                                   [ 1 ]
  1530182-1657613 |                                                   [ 1 ]
  1402750-1530181 |                                                   [ 1 ]
  1275319-1402750 |                                                   [  ]
  1147887-1275318 |*                                                  [ 4 ]
  1020455-1147886 |                                                   [ 3 ]
  893023-1020454  |*                                                  [ 5 ]
  765591-893022   |**                                                 [ 9 ]
  638160-765591   |**                                                 [ 7 ]
  510728-638159   |****                                               [ 16 ]
  383296-510727   |***                                                [ 11 ]
  255864-383295   |******                                             [ 20 ]
  128432-255863   |******                                             [ 20 ]
  1001-128432     |************************************************** [ 161 ]

Storage Throughput = excellent ( 1028.03 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40024757 bp ( 40024757 non ambiguous )
   - Num Contigs Represented = 216
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:15:14 (hh:mm:ss) Elapsed Time
Round Time: 00:29:59 (hh:mm:ss) Elapsed Time : 239 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 00:00:23 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3547 repeats masked totaling 2381485 bp(s).
   - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10030262 bp
       Num Contigs Represented = 113
       Non ambiguous bp:
             Initial: 10030262 bp
             After Masking: 7431737 bp
             Masked: 25.91 % 
 -- Input Database Coverage: 10030262 bp out of 61002793 bp ( 16.44 % )
Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 37675
Comparison Time: 00:04:40 (hh:mm:ss) Elapsed Time, 9491 HSPs Collected
Number of families returned by RECON: 463
Round Time: 00:06:15 (hh:mm:ss) Elapsed Time : 7 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:04 (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...
       11807 repeats masked totaling 8764354 bp(s).
   - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30035295 bp
       Num Contigs Represented = 197
       Non ambiguous bp:
             Initial: 30035295 bp
             After Masking: 20624423 bp
             Masked: 31.33 % 
 -- Input Database Coverage: 40065557 bp out of 61002793 bp ( 65.68 % )
Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 336610
Comparison Time: 00:23:26 (hh:mm:ss) Elapsed Time, 13871 HSPs Collected
Number of families returned by RECON: 2062
Round Time: 00:26:06 (hh:mm:ss) Elapsed Time : 22 families discovered.
   - Increasing sample size to include end piece now = 110972531


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 110972531 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       8147 repeats masked totaling 5332159 bp(s).
   - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 20937022 bp
       Num Contigs Represented = 157
       Non ambiguous bp:
             Initial: 20937022 bp
             After Masking: 15123492 bp
             Masked: 27.77 % 
 -- Input Database Coverage: 61002579 bp out of 61002793 bp ( 100.00 % )
Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 161596
Comparison Time: 00:13:29 (hh:mm:ss) Elapsed Time, 6216 HSPs Collected
Number of families returned by RECON: 1240
Round Time: 00:15:41 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 278 families found


Classification Time: 00:26:48 (hh:mm:ss) Elapsed Time


Program Time: 01:44:49 (hh:mm:ss) Elapsed Time