RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.Y35DZZ/RM_2614425.FriJan311517332025
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: 1738365453
Database = /dev/shm/rModeler.Y35DZZ/GCF_014235925.2_CTRU02v2   - Sequences = 22
  - Bases = 57008971
Storage Throughput = excellent ( 1266.67 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40035488 bp ( 40035488 non ambiguous )
   - Num Contigs Represented = 22
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:06:44 (hh:mm:ss) Elapsed Time
Round Time: 00:11:16 (hh:mm:ss) Elapsed Time : 74 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 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       839 repeats masked totaling 800954 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10036964 bp
       Num Contigs Represented = 21
       Non ambiguous bp:
             Initial: 10036964 bp
             After Masking: 9208911 bp
             Masked: 8.25 % 
 -- Input Database Coverage: 10036964 bp out of 57008971 bp ( 17.61 % )
Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32131
Comparison Time: 00:03:27 (hh:mm:ss) Elapsed Time, 1545 HSPs Collected
Number of families returned by RECON: 532
Round Time: 00:03:47 (hh:mm:ss) Elapsed Time : 3 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2848 repeats masked totaling 2704797 bp(s).
   - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30038542 bp
       Num Contigs Represented = 21
       Non ambiguous bp:
             Initial: 30038542 bp
             After Masking: 27262171 bp
             Masked: 9.24 % 
 -- Input Database Coverage: 40075506 bp out of 57008971 bp ( 70.30 % )
Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 286146
Comparison Time: 00:20:44 (hh:mm:ss) Elapsed Time, 13549 HSPs Collected
Number of families returned by RECON: 2573
Round Time: 01:30:08 (hh:mm:ss) Elapsed Time : 10 families discovered.
   - Increasing sample size to include end piece now = 106972007


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 106972007 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...
       1858 repeats masked totaling 1876410 bp(s).
   - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 16933296 bp
       Num Contigs Represented = 19
       Non ambiguous bp:
             Initial: 16933296 bp
             After Masking: 14999264 bp
             Masked: 11.42 % 
 -- Input Database Coverage: 57008802 bp out of 57008971 bp ( 100.00 % )
Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 90525
Comparison Time: 00:06:08 (hh:mm:ss) Elapsed Time, 3110 HSPs Collected
Number of families returned by RECON: 1043
Round Time: 00:07:16 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 89 families found


Classification Time: 00:07:52 (hh:mm:ss) Elapsed Time


Program Time: 02:00:19 (hh:mm:ss) Elapsed Time