RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.5SxslK/RM_1939576.FriJan310912522025
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: 1738343571
Database = /dev/shm/rModeler.5SxslK/GCA_030295235.1_Fsolaris_ONT_v03   - Sequences = 62
  - Bases = 51725046
Storage Throughput = excellent ( 1624.79 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40017071 bp ( 40017071 non ambiguous )
   - Num Contigs Represented = 61
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:06:56 (hh:mm:ss) Elapsed Time
Round Time: 00:08:08 (hh:mm:ss) Elapsed Time : 118 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2316 repeats masked totaling 488843 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10007825 bp
       Num Contigs Represented = 52
       Non ambiguous bp:
             Initial: 10007825 bp
             After Masking: 9418454 bp
             Masked: 5.89 % 
 -- Input Database Coverage: 10007825 bp out of 51725046 bp ( 19.35 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32640
Comparison Time: 00:02:40 (hh:mm:ss) Elapsed Time, 3843 HSPs Collected
Number of families returned by RECON: 866
Round Time: 00:02:55 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6689 repeats masked totaling 1446287 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30009178 bp
       Num Contigs Represented = 58
       Non ambiguous bp:
             Initial: 30009178 bp
             After Masking: 28215133 bp
             Masked: 5.98 % 
 -- Input Database Coverage: 40017003 bp out of 51725046 bp ( 77.36 % )
Sampling Time: 00:00:27 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 296835
Comparison Time: 00:12:18 (hh:mm:ss) Elapsed Time, 29538 HSPs Collected
Number of families returned by RECON: 3926
Round Time: 00:13:02 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 101717221


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 101717221 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2793 repeats masked totaling 550071 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 11707786 bp
       Num Contigs Represented = 50
       Non ambiguous bp:
             Initial: 11707786 bp
             After Masking: 10981783 bp
             Masked: 6.20 % 
 -- Input Database Coverage: 51724789 bp out of 51725046 bp ( 100.00 % )
Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 44253
Comparison Time: 00:03:15 (hh:mm:ss) Elapsed Time, 3516 HSPs Collected
Number of families returned by RECON: 1037
Round Time: 00:03:29 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 123 families found


Classification Time: 00:02:50 (hh:mm:ss) Elapsed Time


Program Time: 00:30:24 (hh:mm:ss) Elapsed Time