RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.he8Zjj/RM_6232.ThuSep121026472024
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: 1726162006
Database = /dev/shm/rModeler.he8Zjj/GCA_900180395.1_PcyM   - Sequences = 56
  - Bases = 30657612
Storage Throughput = excellent ( 1128.98 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 30657462 bp ( 30657462 non ambiguous )
   - Num Contigs Represented = 56
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:10:21 (hh:mm:ss) Elapsed Time
Round Time: 01:06:25 (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 00:00:50 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1765 repeats masked totaling 1818842 bp(s).
   - TE Masking time 00:01:45 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10030852 bp
       Num Contigs Represented = 37
       Non ambiguous bp:
             Initial: 10030852 bp
             After Masking: 7793743 bp
             Masked: 22.30 % 
 -- Input Database Coverage: 10030852 bp out of 30657612 bp ( 32.72 % )
Sampling Time: 00:02:38 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 34453
Comparison Time: 00:18:44 (hh:mm:ss) Elapsed Time, 8346 HSPs Collected
Number of families returned by RECON: 1143
Round Time: 00:21:38 (hh:mm:ss) Elapsed Time : 2 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 00:01:41 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3728 repeats masked totaling 3834460 bp(s).
   - TE Masking time 00:02:33 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 20626530 bp
       Num Contigs Represented = 50
       Non ambiguous bp:
             Initial: 20626530 bp
             After Masking: 15858594 bp
             Masked: 23.12 % 
 -- Input Database Coverage: 30657382 bp out of 30657612 bp ( 100.00 % )
Sampling Time: 00:04:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 142845
Comparison Time: 01:02:05 (hh:mm:ss) Elapsed Time, 27733 HSPs Collected
Number of families returned by RECON: 3119
Round Time: 01:11:05 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 112 families found


Classification Time: 00:17:40 (hh:mm:ss) Elapsed Time


Program Time: 02:56:48 (hh:mm:ss) Elapsed Time