RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.duKKgn/RM_10694.SunJul71154402024
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: 1720378478
Database = /dev/shm/rModeler.duKKgn/GCF_013426205.1_ASM1342620v1   - Sequences = 7
  - Bases = 37771916
Storage Throughput = excellent ( 1031.85 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37771784 bp ( 37771784 non ambiguous )
   - Num Contigs Represented = 7
   - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:16:08 (hh:mm:ss) Elapsed Time
Round Time: 00:16:59 (hh:mm:ss) Elapsed Time : 46 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 00:00:34 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       734 repeats masked totaling 102183 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10000510 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 10000510 bp
             After Masking: 9865592 bp
             Masked: 1.35 % 
 -- Input Database Coverage: 10000510 bp out of 37771916 bp ( 26.48 % )
Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31125
Comparison Time: 00:17:00 (hh:mm:ss) Elapsed Time, 3736 HSPs Collected
Number of families returned by RECON: 689
Round Time: 03:13:57 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2231 repeats masked totaling 832937 bp(s).
   - TE Masking time 00:01:27 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27771194 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 27771194 bp
             After Masking: 26865530 bp
             Masked: 3.26 % 
 -- Input Database Coverage: 37771704 bp out of 37771916 bp ( 100.00 % )
Sampling Time: 00:03:04 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 243253
Comparison Time: 00:32:07 (hh:mm:ss) Elapsed Time, 17911 HSPs Collected
Number of families returned by RECON: 2985
Round Time: 02:33:56 (hh:mm:ss) Elapsed Time : 20 families discovered.

RepeatScout/RECON discovery complete: 68 families found


Classification Time: 00:02:11 (hh:mm:ss) Elapsed Time


Program Time: 06:07:03 (hh:mm:ss) Elapsed Time