RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.J3CYVO/RM_3366.TueAug130513432024
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: 1723551223
Database = /dev/shm/rModeler.J3CYVO/GCA_014607475.1_ASM1460747v1   - Sequences = 12
  - Bases = 37134214
Storage Throughput = excellent ( 1043.27 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37134081 bp ( 37134081 non ambiguous )
   - Num Contigs Represented = 12
   - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:15:02 (hh:mm:ss) Elapsed Time
Round Time: 19:07:18 (hh:mm:ss) Elapsed Time : 68 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 00:00:34 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       717 repeats masked totaling 622199 bp(s).
   - TE Masking time 00:01:13 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10007387 bp
       Num Contigs Represented = 12
       Non ambiguous bp:
             Initial: 10007387 bp
             After Masking: 9342439 bp
             Masked: 6.64 % 
 -- Input Database Coverage: 10007387 bp out of 37134214 bp ( 26.95 % )
Sampling Time: 00:01:49 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31375
Comparison Time: 00:37:20 (hh:mm:ss) Elapsed Time, 3517 HSPs Collected
Number of families returned by RECON: 733
Round Time: 04:41:07 (hh:mm:ss) Elapsed Time : 3 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2115 repeats masked totaling 2534310 bp(s).
   - TE Masking time 00:13:41 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27126614 bp
       Num Contigs Represented = 12
       Non ambiguous bp:
             Initial: 27126614 bp
             After Masking: 24460946 bp
             Masked: 9.83 % 
 -- Input Database Coverage: 37134001 bp out of 37134214 bp ( 100.00 % )
Sampling Time: 00:15:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 232221
Comparison Time: 01:15:39 (hh:mm:ss) Elapsed Time, 21326 HSPs Collected
Number of families returned by RECON: 2836
Round Time: 07:07:30 (hh:mm:ss) Elapsed Time : 14 families discovered.

RepeatScout/RECON discovery complete: 85 families found


Classification Time: 00:16:14 (hh:mm:ss) Elapsed Time


Program Time: 31:12:09 (hh:mm:ss) Elapsed Time