RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.lQaj0D/RM_29793.TueAug130320282024
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: 1723544428
Database = /dev/shm/rModeler.lQaj0D/GCA_008275145.1_ASM827514v1   - Sequences = 7
  - Bases = 12431639
Storage Throughput = excellent ( 1052.26 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12431558 bp ( 12431558 non ambiguous )
   - Num Contigs Represented = 7
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:06:34 (hh:mm:ss) Elapsed Time
Round Time: 00:06:54 (hh:mm:ss) Elapsed Time : 9 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 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       236 repeats masked totaling 65798 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10016555 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 10016555 bp
             After Masking: 9924423 bp
             Masked: 0.92 % 
 -- Input Database Coverage: 10016555 bp out of 12431639 bp ( 80.57 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31626
Comparison Time: 00:04:58 (hh:mm:ss) Elapsed Time, 2713 HSPs Collected
Number of families returned by RECON: 684
Round Time: 00:05:58 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 32431639


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32431639 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       59 repeats masked totaling 20710 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2414923 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 2414923 bp
             After Masking: 2387077 bp
             Masked: 1.15 % 
 -- Input Database Coverage: 12431478 bp out of 12431639 bp ( 100.00 % )
Sampling Time: 00:00:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1891
Comparison Time: 00:00:44 (hh:mm:ss) Elapsed Time, 157 HSPs Collected
Number of families returned by RECON: 83
Round Time: 00:00:50 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 11 families found


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


Program Time: 00:14:36 (hh:mm:ss) Elapsed Time