RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.jVMUSC/RM_1033278.FriJan311515272025
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: 1738365326
Database = /dev/shm/rModeler.jVMUSC/GCF_000512605.2_ASM51260v3   - Sequences = 11
  - Bases = 20887338
Storage Throughput = excellent ( 1633.21 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 20887198 bp ( 20887198 non ambiguous )
   - Num Contigs Represented = 11
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:02:58 (hh:mm:ss) Elapsed Time
Round Time: 00:03:13 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       35 repeats masked totaling 5657 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10038794 bp
       Num Contigs Represented = 11
       Non ambiguous bp:
             Initial: 10038794 bp
             After Masking: 10011781 bp
             Masked: 0.27 % 
 -- Input Database Coverage: 10038794 bp out of 20887338 bp ( 48.06 % )
Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32131
Comparison Time: 00:05:41 (hh:mm:ss) Elapsed Time, 792 HSPs Collected
Number of families returned by RECON: 428
Round Time: 00:07:08 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 40887338


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40887338 bp
   - Sequence extraction : 00:00:01 (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...
       28 repeats masked totaling 3875 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10848324 bp
       Num Contigs Represented = 11
       Non ambiguous bp:
             Initial: 10848324 bp
             After Masking: 10810034 bp
             Masked: 0.35 % 
 -- Input Database Coverage: 20887118 bp out of 20887338 bp ( 100.00 % )
Sampling Time: 00:00:14 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 36856
Comparison Time: 00:06:22 (hh:mm:ss) Elapsed Time, 982 HSPs Collected
Number of families returned by RECON: 441
Round Time: 00:06:41 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 2 families found


Classification Time: 00:00:26 (hh:mm:ss) Elapsed Time


Program Time: 00:17:28 (hh:mm:ss) Elapsed Time