RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.01cvMJ/RM_17353.TueAug131239352024
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: 1723577973
Database = /dev/shm/rModeler.01cvMJ/GCA_020450195.1_ASM2045019v1   - Sequences = 13
  - Bases = 12727606
Storage Throughput = excellent ( 1060.73 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12727488 bp ( 12727488 non ambiguous )
   - Num Contigs Represented = 13
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:07:13 (hh:mm:ss) Elapsed Time
Round Time: 00:08:13 (hh:mm:ss) Elapsed Time : 16 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 00:00:25 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       343 repeats masked totaling 78309 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10005400 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 10005400 bp
             After Masking: 9645583 bp
             Masked: 3.60 % 
 -- Input Database Coverage: 10005400 bp out of 12727606 bp ( 78.61 % )
Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32131
Comparison Time: 00:05:09 (hh:mm:ss) Elapsed Time, 2620 HSPs Collected
Number of families returned by RECON: 727
Round Time: 00:05:47 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 32727606


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32727606 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...
       70 repeats masked totaling 19038 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2722085 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 2722085 bp
             After Masking: 2651277 bp
             Masked: 2.60 % 
 -- Input Database Coverage: 12727485 bp out of 12727606 bp ( 100.00 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2415
Comparison Time: 00:00:53 (hh:mm:ss) Elapsed Time, 171 HSPs Collected
Number of families returned by RECON: 101
Round Time: 00:01:01 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 17 families found


Classification Time: 00:00:30 (hh:mm:ss) Elapsed Time


Program Time: 00:15:31 (hh:mm:ss) Elapsed Time