RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.BlUyVE/RM_1520.TueAug130130282024
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: 1723537827
Database = /dev/shm/rModeler.BlUyVE/GCA_004115165.2_Cimm211_ragoo   - Sequences = 62
  - Bases = 27474893
Storage Throughput = good ( 703.09 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 27474817 bp ( 27451317 non ambiguous )
   - Num Contigs Represented = 62
   - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:08:00 (hh:mm:ss) Elapsed Time
Round Time: 00:16:11 (hh:mm:ss) Elapsed Time : 44 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       941 repeats masked totaling 918478 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10041423 bp
       Num Contigs Represented = 24
       Non ambiguous bp:
             Initial: 10032523 bp
             After Masking: 9087746 bp
             Masked: 9.42 % 
 -- Input Database Coverage: 10041423 bp out of 27474893 bp ( 36.55 % )
Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 36046
Comparison Time: 00:05:05 (hh:mm:ss) Elapsed Time, 10527 HSPs Collected
Number of families returned by RECON: 546
Round Time: 00:10:14 (hh:mm:ss) Elapsed Time : 4 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 00:00:26 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2060 repeats masked totaling 2313343 bp(s).
   - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 17433369 bp
       Num Contigs Represented = 45
       Non ambiguous bp:
             Initial: 17418769 bp
             After Masking: 15026727 bp
             Masked: 13.73 % 
 -- Input Database Coverage: 27474792 bp out of 27474893 bp ( 100.00 % )
Sampling Time: 00:00:43 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 112575
Comparison Time: 00:11:36 (hh:mm:ss) Elapsed Time, 6632 HSPs Collected
Number of families returned by RECON: 1090
Round Time: 00:13:19 (hh:mm:ss) Elapsed Time : 4 families discovered.

RepeatScout/RECON discovery complete: 52 families found


Classification Time: 00:09:45 (hh:mm:ss) Elapsed Time


Program Time: 00:49:29 (hh:mm:ss) Elapsed Time