RepeatModeler Version 2.0.5
===========================
Using output directory = /suikou/files/m768/yoshitake.kazutoshi/work/saka/test/RM_1.WedNov290306152023
Search Engine = rmblast 2.14.1+
Threads = 8
Dependencies: TRF 4.09, RECON 1.08, RepeatScout 1.0.6, RepeatMasker 4.1.5
LTR Structural Analysis: Enabled ( GenomeTools 1.6.4, LTR_Retriever v2.9.0,
                                   Ninja 0.97-cluster_only, MAFFT 7.471,
                                   CD-HIT 4.8.1 )
Random Number Seed: 1701227171
Database = /suikou/files/m768/yoshitake.kazutoshi/work/saka/test/genome1   - Sequences = 1
  - Bases = 4641652
Storage Throughput = excellent ( 1475.04 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 4641587 bp ( 4641587 non ambiguous )
   - Num Contigs Represented = 1
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:00:48 (hh:mm:ss) Elapsed Time
Round Time: 00:01:20 (hh:mm:ss) Elapsed Time : 7 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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       363 repeats masked totaling 31634 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4641587 bp
       Num Contigs Represented = 1
       Non ambiguous bp:
             Initial: 4641587 bp
             After Masking: 4605100 bp
             Masked: 0.79 % 
 -- Input Database Coverage: 4641587 bp out of 4641652 bp ( 100.00 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 6786
Comparison Time: 00:07:49 (hh:mm:ss) Elapsed Time, 2219 HSPs Collected
Number of families returned by RECON: 622
Round Time: 00:08:05 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 7 families found


LTR Structural Analysis
=======================
LTRPipeline Time: 00:00:24 (hh:mm:ss) Elapsed Time


Classification Time: 00:00:43 (hh:mm:ss) Elapsed Time


Program Time: 00:10:32 (hh:mm:ss) Elapsed Time