RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.KXu7Vq/RM_7838.TueAug130430162024
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: 1723548615
Database = /dev/shm/rModeler.KXu7Vq/GCA_013177555.1_ASM1317755v1   - Sequences = 7
  - Bases = 14609527
Storage Throughput = excellent ( 1068.16 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14609391 bp ( 14609391 non ambiguous )
   - Num Contigs Represented = 7
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:10:26 (hh:mm:ss) Elapsed Time
Round Time: 00:11:58 (hh:mm:ss) Elapsed Time : 20 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 00:00:29 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       333 repeats masked totaling 164897 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10014974 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 10014974 bp
             After Masking: 9707166 bp
             Masked: 3.07 % 
 -- Input Database Coverage: 10014974 bp out of 14609527 bp ( 68.55 % )
Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31626
Comparison Time: 00:08:46 (hh:mm:ss) Elapsed Time, 3686 HSPs Collected
Number of families returned by RECON: 927
Round Time: 00:09:27 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 34609527


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34609527 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       118 repeats masked totaling 48922 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4594410 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 4594410 bp
             After Masking: 4484667 bp
             Masked: 2.39 % 
 -- Input Database Coverage: 14609384 bp out of 14609527 bp ( 100.00 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 6670
Comparison Time: 00:02:33 (hh:mm:ss) Elapsed Time, 701 HSPs Collected
Number of families returned by RECON: 295
Round Time: 00:02:52 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 20 families found


Classification Time: 00:00:53 (hh:mm:ss) Elapsed Time


Program Time: 00:25:10 (hh:mm:ss) Elapsed Time