RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.LW4wVL/RM_3964327.SatFeb151049432025
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: 1739645383
Database = /dev/shm/rModeler.LW4wVL/GCA_964212145.1_pySymPilo4.1_alternate_haplotype   - Sequences = 1070
  - Bases = 109538490
  - N50 = 215877
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  982420-1052394  |                                                   [ 2 ]
  912446-982419   |                                                   [  ]
  842472-912445   |                                                   [  ]
  772498-842471   |                                                   [ 1 ]
  702524-772497   |                                                   [ 4 ]
  632550-702523   |                                                   [ 3 ]
  562576-632549   |                                                   [ 7 ]
  492602-562575   |                                                   [ 11 ]
  422628-492601   |*                                                  [ 16 ]
  352654-422627   |*                                                  [ 15 ]
  282680-352653   |**                                                 [ 35 ]
  212706-282679   |****                                               [ 59 ]
  142732-212705   |********                                           [ 108 ]
  72758-142731    |*************                                      [ 175 ]
  2785-72758      |************************************************** [ 634 ]

Storage Throughput = excellent ( 1808.54 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40001395 bp ( 40001395 non ambiguous )
   - Num Contigs Represented = 636
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:05:54 (hh:mm:ss) Elapsed Time
Round Time: 00:10:57 (hh:mm:ss) Elapsed Time : 352 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 00:00:21 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       17745 repeats masked totaling 2116301 bp(s).
   - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10036683 bp
       Num Contigs Represented = 241
       Non ambiguous bp:
             Initial: 10036683 bp
             After Masking: 7337650 bp
             Masked: 26.89 % 
 -- Input Database Coverage: 10036683 bp out of 109538490 bp ( 9.16 % )
Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 40755
Comparison Time: 00:03:16 (hh:mm:ss) Elapsed Time, 6129 HSPs Collected
Number of families returned by RECON: 1061
Round Time: 00:03:58 (hh:mm:ss) Elapsed Time : 5 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       57407 repeats masked totaling 6872799 bp(s).
   - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30007168 bp
       Num Contigs Represented = 537
       Non ambiguous bp:
             Initial: 30007168 bp
             After Masking: 21351328 bp
             Masked: 28.85 % 
 -- Input Database Coverage: 40043851 bp out of 109538490 bp ( 36.56 % )
Sampling Time: 00:01:44 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 409965
Comparison Time: 00:14:00 (hh:mm:ss) Elapsed Time, 40413 HSPs Collected
Number of families returned by RECON: 4031
Round Time: 00:17:35 (hh:mm:ss) Elapsed Time : 45 families discovered.


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 90000000 bp
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:03:33 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       135391 repeats masked totaling 16863809 bp(s).
   - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 69494441 bp
       Num Contigs Represented = 850
       Non ambiguous bp:
             Initial: 69494441 bp
             After Masking: 48511948 bp
             Masked: 30.19 % 
 -- Input Database Coverage: 109538292 bp out of 109538490 bp ( 100.00 % )
Sampling Time: 00:04:33 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2189278
Comparison Time: 00:48:21 (hh:mm:ss) Elapsed Time, 127861 HSPs Collected
Number of families returned by RECON: 11617
Round Time: 00:56:02 (hh:mm:ss) Elapsed Time : 168 families discovered.

RepeatScout/RECON discovery complete: 570 families found


Classification Time: 00:17:46 (hh:mm:ss) Elapsed Time


Program Time: 01:46:18 (hh:mm:ss) Elapsed Time