RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.MX6gRV/RM_339439.ThuSep120837392024
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: 1726155458
Database = /dev/shm/rModeler.MX6gRV/GCA_002140095.1_PKNOHv1   - Sequences = 28
  - Bases = 24771595
Storage Throughput = excellent ( 1092.61 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 24771559 bp ( 24767879 non ambiguous )
   - Num Contigs Represented = 28
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:09:04 (hh:mm:ss) Elapsed Time
Round Time: 00:25:34 (hh:mm:ss) Elapsed Time : 103 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 00:02:57 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4372 repeats masked totaling 646783 bp(s).
   - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10019529 bp
       Num Contigs Represented = 20
       Non ambiguous bp:
             Initial: 10017349 bp
             After Masking: 8371476 bp
             Masked: 16.43 % 
 -- Input Database Coverage: 10019529 bp out of 24771595 bp ( 40.45 % )
Sampling Time: 00:03:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32131
Comparison Time: 00:36:51 (hh:mm:ss) Elapsed Time, 22095 HSPs Collected
Number of families returned by RECON: 1543
Round Time: 00:41:49 (hh:mm:ss) Elapsed Time : 13 families discovered.
   - Increasing sample size to include end piece now = 44771595


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 44771595 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:03:48 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5632 repeats masked totaling 906385 bp(s).
   - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 14751999 bp
       Num Contigs Represented = 22
       Non ambiguous bp:
             Initial: 14750499 bp
             After Masking: 12600642 bp
             Masked: 14.57 % 
 -- Input Database Coverage: 24771528 bp out of 24771595 bp ( 100.00 % )
Sampling Time: 00:04:35 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 72390
Comparison Time: 00:59:30 (hh:mm:ss) Elapsed Time, 20413 HSPs Collected
Number of families returned by RECON: 2584
Round Time: 01:05:35 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 125 families found


Classification Time: 00:05:52 (hh:mm:ss) Elapsed Time


Program Time: 02:18:50 (hh:mm:ss) Elapsed Time