RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.egakOG/RM_16484.ThuSep121123242024
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: 1726165404
Database = /dev/shm/rModeler.egakOG/GCA_900090025.2_PowCR01   - Sequences = 779
  - Bases = 33529622
  - N50 = 1146583
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2856941-3060936 |                                                   [ 2 ]
  2652946-2856941 |                                                   [  ]
  2448951-2652946 |                                                   [  ]
  2244956-2448951 |                                                   [ 1 ]
  2040961-2244956 |                                                   [  ]
  1836966-2040961 |                                                   [ 2 ]
  1632971-1836966 |                                                   [  ]
  1428976-1632971 |                                                   [ 1 ]
  1224981-1428976 |                                                   [ 1 ]
  1020986-1224981 |                                                   [ 1 ]
  816991-1020986  |                                                   [ 2 ]
  612996-816991   |                                                   [ 3 ]
  409001-612996   |                                                   [ 1 ]
  205006-409001   |                                                   [ 1 ]
  1011-205006     |************************************************** [ 764 ]

Storage Throughput = excellent ( 1140.85 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 33529464 bp ( 33268675 non ambiguous )
   - Num Contigs Represented = 779
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:13:03 (hh:mm:ss) Elapsed Time
Round Time: 01:23:57 (hh:mm:ss) Elapsed Time : 115 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 00:01:00 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1153 repeats masked totaling 1085823 bp(s).
   - TE Masking time 00:01:33 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10108903 bp
       Num Contigs Represented = 244
       Non ambiguous bp:
             Initial: 10004216 bp
             After Masking: 8573326 bp
             Masked: 14.30 % 
 -- Input Database Coverage: 10108903 bp out of 33529622 bp ( 30.15 % )
Sampling Time: 00:02:36 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 84666
Comparison Time: 00:44:39 (hh:mm:ss) Elapsed Time, 20552 HSPs Collected
Number of families returned by RECON: 1362
Round Time: 00:48:48 (hh:mm:ss) Elapsed Time : 9 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 00:02:19 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4779 repeats masked totaling 2928945 bp(s).
   - TE Masking time 00:02:48 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 23420501 bp
       Num Contigs Represented = 590
       Non ambiguous bp:
             Initial: 23264399 bp
             After Masking: 19621064 bp
             Masked: 15.66 % 
 -- Input Database Coverage: 33529404 bp out of 33529622 bp ( 100.00 % )
Sampling Time: 00:05:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 500500
Comparison Time: 02:53:35 (hh:mm:ss) Elapsed Time, 17656 HSPs Collected
Number of families returned by RECON: 2918
Round Time: 03:05:22 (hh:mm:ss) Elapsed Time : 22 families discovered.

RepeatScout/RECON discovery complete: 146 families found


Classification Time: 00:16:35 (hh:mm:ss) Elapsed Time


Program Time: 05:34:42 (hh:mm:ss) Elapsed Time