RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.1YKi17/RM_18417.WedSep181039572024
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: 1726681197
Database = /dev/shm/rModeler.1YKi17/GCA_001720245.2_ASM172024v2   - Sequences = 8
  - Bases = 16328170
Storage Throughput = excellent ( 1093.07 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 16328046 bp ( 16328045 non ambiguous )
   - Num Contigs Represented = 8
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:08:48 (hh:mm:ss) Elapsed Time
Round Time: 00:14:06 (hh:mm:ss) Elapsed Time : 71 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...
       1802 repeats masked totaling 632939 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10018560 bp
       Num Contigs Represented = 8
       Non ambiguous bp:
             Initial: 10018559 bp
             After Masking: 9371429 bp
             Masked: 6.46 % 
 -- Input Database Coverage: 10018560 bp out of 16328170 bp ( 61.36 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31626
Comparison Time: 00:04:30 (hh:mm:ss) Elapsed Time, 1588 HSPs Collected
Number of families returned by RECON: 469
Round Time: 00:05:01 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 36328170


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 36328170 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...
       1263 repeats masked totaling 528505 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 6309467 bp
       Num Contigs Represented = 8
       Non ambiguous bp:
             Initial: 6309467 bp
             After Masking: 5770579 bp
             Masked: 8.54 % 
 -- Input Database Coverage: 16328027 bp out of 16328170 bp ( 100.00 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 12561
Comparison Time: 00:02:18 (hh:mm:ss) Elapsed Time, 660 HSPs Collected
Number of families returned by RECON: 223
Round Time: 00:02:37 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 74 families found


Classification Time: 00:06:03 (hh:mm:ss) Elapsed Time


Program Time: 00:27:47 (hh:mm:ss) Elapsed Time