RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.hNzV7k/RM_15105.MonAug121815122024
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: 1723511710
Database = /dev/shm/rModeler.hNzV7k/GCA_001189475.1_ASM118947v1   - Sequences = 99
  - Bases = 12498763
Storage Throughput = excellent ( 1043.23 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12498655 bp ( 12332798 non ambiguous )
   - Num Contigs Represented = 99
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:06:39 (hh:mm:ss) Elapsed Time
Round Time: 00:06:52 (hh:mm:ss) Elapsed Time : 5 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 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       112 repeats masked totaling 13020 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10163326 bp
       Num Contigs Represented = 92
       Non ambiguous bp:
             Initial: 10029236 bp
             After Masking: 9994564 bp
             Masked: 0.35 % 
 -- Input Database Coverage: 10163326 bp out of 12498763 bp ( 81.31 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 45753
Comparison Time: 00:06:23 (hh:mm:ss) Elapsed Time, 2986 HSPs Collected
Number of families returned by RECON: 757
Round Time: 00:07:06 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 32498763


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32498763 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       61 repeats masked totaling 6693 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2335249 bp
       Num Contigs Represented = 40
       Non ambiguous bp:
             Initial: 2303482 bp
             After Masking: 2290754 bp
             Masked: 0.55 % 
 -- Input Database Coverage: 12498575 bp out of 12498763 bp ( 100.00 % )
Sampling Time: 00:00:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2145
Comparison Time: 00:00:50 (hh:mm:ss) Elapsed Time, 164 HSPs Collected
Number of families returned by RECON: 79
Round Time: 00:00:55 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 9 families found


Classification Time: 00:00:24 (hh:mm:ss) Elapsed Time


Program Time: 00:15:17 (hh:mm:ss) Elapsed Time