RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.BsdHEf/RM_9897.TueSep171127322024
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: 1726597651
Database = /dev/shm/rModeler.BsdHEf/GCA_917563895.1_Assembly_1   - Sequences = 18523
  - Bases = 25196438
  - N50 = 15790
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  162711-174327 |                                                   [ 1 ]
  151096-162711 |                                                   [  ]
  139481-151096 |                                                   [  ]
  127866-139481 |                                                   [  ]
  116251-127866 |                                                   [ 1 ]
  104636-116251 |                                                   [ 2 ]
  93021-104636  |                                                   [ 1 ]
  81405-93020   |                                                   [ 7 ]
  69790-81405   |                                                   [ 11 ]
  58175-69790   |                                                   [ 22 ]
  46560-58175   |                                                   [ 28 ]
  34945-46560   |                                                   [ 52 ]
  23330-34945   |                                                   [ 94 ]
  11715-23330   |                                                   [ 250 ]
  100-11715     |************************************************** [ 18054 ]

Storage Throughput = excellent ( 1076.00 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 25196240 bp ( 23309532 non ambiguous )
   - Num Contigs Represented = 18522
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:09:39 (hh:mm:ss) Elapsed Time
Round Time: 00:23:45 (hh:mm:ss) Elapsed Time : 83 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 00:00:46 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3313 repeats masked totaling 890169 bp(s).
   - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10869981 bp
       Num Contigs Represented = 8076
       Non ambiguous bp:
             Initial: 10007754 bp
             After Masking: 9078538 bp
             Masked: 9.28 % 
 -- Input Database Coverage: 10869981 bp out of 25196438 bp ( 43.14 % )
Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32768560
Comparison Time: 00:40:08 (hh:mm:ss) Elapsed Time, 59417 HSPs Collected
Number of families returned by RECON: 1297
Round Time: 00:48:07 (hh:mm:ss) Elapsed Time : 23 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 00:00:59 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6427 repeats masked totaling 1748929 bp(s).
   - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 14326225 bp
       Num Contigs Represented = 10502
       Non ambiguous bp:
             Initial: 13301744 bp
             After Masking: 11501427 bp
             Masked: 13.53 % 
 -- Input Database Coverage: 25196206 bp out of 25196438 bp ( 100.00 % )
Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 55551070
Comparison Time: 00:50:52 (hh:mm:ss) Elapsed Time, 13774 HSPs Collected
Number of families returned by RECON: 1931
Round Time: 00:53:23 (hh:mm:ss) Elapsed Time : 15 families discovered.

RepeatScout/RECON discovery complete: 121 families found


Classification Time: 00:06:40 (hh:mm:ss) Elapsed Time


Program Time: 02:11:55 (hh:mm:ss) Elapsed Time