RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.BeacLS/RM_26803.MonMay271128112024
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: 1716834490
Database = /dev/shm/rModeler.BeacLS/GCF_028828025.1_ASM2882802v1   - Sequences = 5
  - Bases = 30363515
Storage Throughput = excellent ( 1038.77 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 30363376 bp ( 30363376 non ambiguous )
   - Num Contigs Represented = 5
   - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:10:16 (hh:mm:ss) Elapsed Time
Round Time: 00:12:05 (hh:mm:ss) Elapsed Time : 89 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1056 repeats masked totaling 343917 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10030632 bp
       Num Contigs Represented = 4
       Non ambiguous bp:
             Initial: 10030632 bp
             After Masking: 9647487 bp
             Masked: 3.82 % 
 -- Input Database Coverage: 10030632 bp out of 30363515 bp ( 33.04 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31375
Comparison Time: 00:04:23 (hh:mm:ss) Elapsed Time, 2588 HSPs Collected
Number of families returned by RECON: 889
Round Time: 00:05:07 (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 00:00:21 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1807 repeats masked totaling 545355 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 20332664 bp
       Num Contigs Represented = 5
       Non ambiguous bp:
             Initial: 20332664 bp
             After Masking: 19723652 bp
             Masked: 3.00 % 
 -- Input Database Coverage: 30363296 bp out of 30363515 bp ( 100.00 % )
Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 129795
Comparison Time: 00:13:04 (hh:mm:ss) Elapsed Time, 8672 HSPs Collected
Number of families returned by RECON: 2647
Round Time: 00:14:01 (hh:mm:ss) Elapsed Time : 6 families discovered.

RepeatScout/RECON discovery complete: 97 families found


Classification Time: 00:04:54 (hh:mm:ss) Elapsed Time


Program Time: 00:36:07 (hh:mm:ss) Elapsed Time