RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.zDL0AC/RM_29503.SunJul71148462024
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: 1720378124
Database = /dev/shm/rModeler.zDL0AC/GCF_019434415.1_Coph_MacrARSEF324_H1_v1.0   - Sequences = 36
  - Bases = 44811144
Storage Throughput = excellent ( 1033.35 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40029646 bp ( 40029523 non ambiguous )
   - Num Contigs Represented = 36
   - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:16:31 (hh:mm:ss) Elapsed Time
Round Time: 16:28:05 (hh:mm:ss) Elapsed Time : 101 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 00:00:38 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1621 repeats masked totaling 1492158 bp(s).
   - TE Masking time 00:05:20 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10022083 bp
       Num Contigs Represented = 33
       Non ambiguous bp:
             Initial: 10022083 bp
             After Masking: 8509884 bp
             Masked: 15.09 % 
 -- Input Database Coverage: 10022083 bp out of 44811144 bp ( 22.37 % )
Sampling Time: 00:06:01 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32385
Comparison Time: 00:21:31 (hh:mm:ss) Elapsed Time, 4858 HSPs Collected
Number of families returned by RECON: 504
Round Time: 07:30:26 (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 00:01:59 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5405 repeats masked totaling 5706805 bp(s).
   - TE Masking time 00:29:17 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30007483 bp
       Num Contigs Represented = 35
       Non ambiguous bp:
             Initial: 30007360 bp
             After Masking: 24233493 bp
             Masked: 19.24 % 
 -- Input Database Coverage: 40029566 bp out of 44811144 bp ( 89.33 % )
Sampling Time: 00:31:23 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 290703
Comparison Time: 00:26:56 (hh:mm:ss) Elapsed Time, 16341 HSPs Collected
Number of families returned by RECON: 2503
Round Time: 01:29:40 (hh:mm:ss) Elapsed Time : 24 families discovered.
   - Increasing sample size to include end piece now = 94789061


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 94789061 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       942 repeats masked totaling 1002972 bp(s).
   - TE Masking time 00:08:40 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4781352 bp
       Num Contigs Represented = 29
       Non ambiguous bp:
             Initial: 4781352 bp
             After Masking: 3770457 bp
             Masked: 21.14 % 
 -- Input Database Coverage: 44810918 bp out of 44811144 bp ( 100.00 % )
Sampling Time: 00:09:00 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 7021
Comparison Time: 00:01:55 (hh:mm:ss) Elapsed Time, 271 HSPs Collected
Number of families returned by RECON: 171
Round Time: 00:10:57 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 129 families found


Classification Time: 00:15:58 (hh:mm:ss) Elapsed Time


Program Time: 25:55:06 (hh:mm:ss) Elapsed Time