RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.GPbxrM/RM_352.TueAug130451582024
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: 1723549917
Database = /dev/shm/rModeler.GPbxrM/GCA_014183025.1_ASM1418302v1   - Sequences = 169
  - Bases = 34626204
  - N50 = 3543479
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  4578357-4905312 |                                                   [ 1 ]
  4251403-4578357 |                                                   [  ]
  3924449-4251403 |                                                   [  ]
  3597495-3924449 |                                                   [ 2 ]
  3270541-3597495 |                                                   [ 1 ]
  2943587-3270541 |                                                   [ 1 ]
  2616633-2943587 |                                                   [  ]
  2289679-2616633 |                                                   [  ]
  1962725-2289679 |                                                   [  ]
  1635771-1962725 |                                                   [ 2 ]
  1308817-1635771 |                                                   [ 2 ]
  981863-1308817  |                                                   [ 1 ]
  654909-981863   |*                                                  [ 5 ]
  327955-654909   |                                                   [ 2 ]
  1001-327955     |************************************************** [ 152 ]

Storage Throughput = excellent ( 1049.84 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 34626092 bp ( 34305657 non ambiguous )
   - Num Contigs Represented = 169
   - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:15:50 (hh:mm:ss) Elapsed Time
Round Time: 00:22:10 (hh:mm:ss) Elapsed Time : 106 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1237 repeats masked totaling 682643 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10087917 bp
       Num Contigs Represented = 69
       Non ambiguous bp:
             Initial: 10014207 bp
             After Masking: 9278397 bp
             Masked: 7.35 % 
 -- Input Database Coverage: 10087917 bp out of 34626204 bp ( 29.13 % )
Sampling Time: 00:00:26 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 42486
Comparison Time: 00:08:27 (hh:mm:ss) Elapsed Time, 2765 HSPs Collected
Number of families returned by RECON: 1029
Round Time: 00:09:02 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2915 repeats masked totaling 1569125 bp(s).
   - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 24538095 bp
       Num Contigs Represented = 127
       Non ambiguous bp:
             Initial: 24291370 bp
             After Masking: 22592676 bp
             Masked: 6.99 % 
 -- Input Database Coverage: 34626012 bp out of 34626204 bp ( 100.00 % )
Sampling Time: 00:01:02 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 242556
Comparison Time: 00:40:31 (hh:mm:ss) Elapsed Time, 14134 HSPs Collected
Number of families returned by RECON: 3322
Round Time: 00:42:29 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 119 families found


Classification Time: 00:10:17 (hh:mm:ss) Elapsed Time


Program Time: 01:23:58 (hh:mm:ss) Elapsed Time