RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.4dpQxJ/RM_2294300.FriAug231330222024
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: 1724445021
Database = /dev/shm/rModeler.4dpQxJ/GCF_900002385.2_GCA_900002385   - Sequences = 16
  - Bases = 23078472
Storage Throughput = good ( 997.35 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 23078357 bp ( 23078357 non ambiguous )
   - Num Contigs Represented = 16
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:06:27 (hh:mm:ss) Elapsed Time
Round Time: 00:59:14 (hh:mm:ss) Elapsed Time : 56 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 00:01:47 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3419 repeats masked totaling 2338314 bp(s).
   - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10005271 bp
       Num Contigs Represented = 15
       Non ambiguous bp:
             Initial: 10005271 bp
             After Masking: 7288352 bp
             Masked: 27.15 % 
 -- Input Database Coverage: 10005271 bp out of 23078472 bp ( 43.35 % )
Sampling Time: 00:02:32 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32640
Comparison Time: 00:34:52 (hh:mm:ss) Elapsed Time, 619 HSPs Collected
Number of families returned by RECON: 202
Round Time: 00:37:30 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 43078472


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 43078472 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:02:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3732 repeats masked totaling 2583208 bp(s).
   - TE Masking time 00:01:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 13073006 bp
       Num Contigs Represented = 15
       Non ambiguous bp:
             Initial: 13073006 bp
             After Masking: 10028623 bp
             Masked: 23.29 % 
 -- Input Database Coverage: 23078277 bp out of 23078472 bp ( 100.00 % )
Sampling Time: 00:03:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 53956
Comparison Time: 01:12:30 (hh:mm:ss) Elapsed Time, 787 HSPs Collected
Number of families returned by RECON: 241
Round Time: 01:16:01 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 59 families found


Classification Time: 00:06:02 (hh:mm:ss) Elapsed Time


Program Time: 02:58:47 (hh:mm:ss) Elapsed Time