RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.22BPcW/RM_11626.WedAug141249172024
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: 1723664957
Database = /dev/shm/rModeler.22BPcW/GCA_002287245.1_ASM228724v1   - Sequences = 536
  - Bases = 41233446
  - N50 = 430775
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1831687-1962300 |                                                   [ 1 ]
  1701074-1831686 |                                                   [ 1 ]
  1570462-1701074 |                                                   [ 1 ]
  1439849-1570461 |                                                   [ 1 ]
  1309237-1439849 |                                                   [ 1 ]
  1178624-1309236 |                                                   [ 1 ]
  1048011-1178623 |                                                   [ 1 ]
  917399-1048011  |                                                   [ 1 ]
  786786-917398   |                                                   [ 5 ]
  656174-786786   |                                                   [ 1 ]
  525561-656173   |                                                   [ 2 ]
  394948-525560   |                                                   [ 8 ]
  264336-394948   |                                                   [ 9 ]
  133723-264335   |**                                                 [ 25 ]
  3111-133723     |************************************************** [ 478 ]

Storage Throughput = good ( 957.90 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40028881 bp ( 40028881 non ambiguous )
   - Num Contigs Represented = 528
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:20:20 (hh:mm:ss) Elapsed Time
Round Time: 00:54:16 (hh:mm:ss) Elapsed Time : 242 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 00:00:40 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3086 repeats masked totaling 3603045 bp(s).
   - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10011274 bp
       Num Contigs Represented = 196
       Non ambiguous bp:
             Initial: 10011274 bp
             After Masking: 5450885 bp
             Masked: 45.55 % 
 -- Input Database Coverage: 10011274 bp out of 41233446 bp ( 24.28 % )
Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 54615
Comparison Time: 00:05:17 (hh:mm:ss) Elapsed Time, 2458 HSPs Collected
Number of families returned by RECON: 240
Round Time: 00:06:42 (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 : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       9472 repeats masked totaling 11204815 bp(s).
   - TE Masking time 00:01:33 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30017577 bp
       Num Contigs Represented = 425
       Non ambiguous bp:
             Initial: 30017577 bp
             After Masking: 16673183 bp
             Masked: 44.46 % 
 -- Input Database Coverage: 40028851 bp out of 41233446 bp ( 97.08 % )
Sampling Time: 00:03:23 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 478731
Comparison Time: 00:22:53 (hh:mm:ss) Elapsed Time, 11805 HSPs Collected
Number of families returned by RECON: 1009
Round Time: 00:26:43 (hh:mm:ss) Elapsed Time : 10 families discovered.
   - Increasing sample size to include end piece now = 91222172


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 91222172 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       327 repeats masked totaling 347226 bp(s).
   - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 1204461 bp
       Num Contigs Represented = 27
       Non ambiguous bp:
             Initial: 1204461 bp
             After Masking: 779847 bp
             Masked: 35.25 % 
 -- Input Database Coverage: 41233312 bp out of 41233446 bp ( 100.00 % )
Sampling Time: 00:00:14 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 561
Comparison Time: 00:00:27 (hh:mm:ss) Elapsed Time, 7 HSPs Collected
Round Time: 00:00:41 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 254 families found


Classification Time: 00:50:42 (hh:mm:ss) Elapsed Time


Program Time: 02:19:04 (hh:mm:ss) Elapsed Time