RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.juHPhx/RM_273271.WedSep181607522024
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: 1726700871
Database = /dev/shm/rModeler.juHPhx/GCA_002219185.1_ASM221918v1   - Sequences = 19
  - Bases = 12729188
Storage Throughput = good ( 940.03 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12729049 bp ( 12729049 non ambiguous )
   - Num Contigs Represented = 19
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:04:35 (hh:mm:ss) Elapsed Time
Round Time: 00:06:09 (hh:mm:ss) Elapsed Time : 15 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 00:00:21 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       347 repeats masked totaling 142331 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10024211 bp
       Num Contigs Represented = 18
       Non ambiguous bp:
             Initial: 10024211 bp
             After Masking: 9596239 bp
             Masked: 4.27 % 
 -- Input Database Coverage: 10024211 bp out of 12729188 bp ( 78.75 % )
Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33411
Comparison Time: 00:03:59 (hh:mm:ss) Elapsed Time, 2539 HSPs Collected
Number of families returned by RECON: 759
Round Time: 00:04:27 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 32729188


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32729188 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       81 repeats masked totaling 40882 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2704778 bp
       Num Contigs Represented = 14
       Non ambiguous bp:
             Initial: 2704778 bp
             After Masking: 2621992 bp
             Masked: 3.06 % 
 -- Input Database Coverage: 12728989 bp out of 12729188 bp ( 100.00 % )
Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2278
Comparison Time: 00:00:47 (hh:mm:ss) Elapsed Time, 207 HSPs Collected
Number of families returned by RECON: 106
Round Time: 00:00:54 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 16 families found


Classification Time: 00:00:37 (hh:mm:ss) Elapsed Time


Program Time: 00:12:07 (hh:mm:ss) Elapsed Time