RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.9TuXBP/RM_1881277.SunJun301918342024
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: 1719800313
Database = /dev/shm/rModeler.9TuXBP/GCF_027942845.1_ASM2794284v1   - Sequences = 46
  - Bases = 49445812
Storage Throughput = excellent ( 1257.04 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40021828 bp ( 40021818 non ambiguous )
   - Num Contigs Represented = 40
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:12:44 (hh:mm:ss) Elapsed Time
Round Time: 00:25:04 (hh:mm:ss) Elapsed Time : 18 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 00:00:16 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       188 repeats masked totaling 63094 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10017828 bp
       Num Contigs Represented = 25
       Non ambiguous bp:
             Initial: 10017828 bp
             After Masking: 9940316 bp
             Masked: 0.77 % 
 -- Input Database Coverage: 10017828 bp out of 49445812 bp ( 20.26 % )
Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32640
Comparison Time: 00:08:05 (hh:mm:ss) Elapsed Time, 908 HSPs Collected
Number of families returned by RECON: 451
Round Time: 00:14:38 (hh:mm:ss) Elapsed Time : 0 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 00:00:51 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       551 repeats masked totaling 167191 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30003920 bp
       Num Contigs Represented = 36
       Non ambiguous bp:
             Initial: 30003910 bp
             After Masking: 29787207 bp
             Masked: 0.72 % 
 -- Input Database Coverage: 40021748 bp out of 49445812 bp ( 80.94 % )
Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 293761
Comparison Time: 00:58:19 (hh:mm:ss) Elapsed Time, 13634 HSPs Collected
Number of families returned by RECON: 2685
Round Time: 01:54:04 (hh:mm:ss) Elapsed Time : 7 families discovered.
   - Increasing sample size to include end piece now = 99427984


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 99427984 bp
   - Sequence extraction : 00:00:02 (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...
       305 repeats masked totaling 181509 bp(s).
   - TE Masking time 00:01:54 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9423817 bp
       Num Contigs Represented = 29
       Non ambiguous bp:
             Initial: 9423817 bp
             After Masking: 9226476 bp
             Masked: 2.09 % 
 -- Input Database Coverage: 49445565 bp out of 49445812 bp ( 100.00 % )
Sampling Time: 00:02:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 29646
Comparison Time: 00:19:14 (hh:mm:ss) Elapsed Time, 1778 HSPs Collected
Number of families returned by RECON: 444
Round Time: 00:21:34 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 25 families found


Classification Time: 00:02:43 (hh:mm:ss) Elapsed Time


Program Time: 02:58:03 (hh:mm:ss) Elapsed Time