RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.4QA85v/RM_2402245.SunJun302142492024
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: 1719808968
Database = /dev/shm/rModeler.4QA85v/GCF_010111755.1_ASM1011175v1   - Sequences = 13
  - Bases = 12726212
Storage Throughput = good ( 835.58 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12726060 bp ( 12725060 non ambiguous )
   - Num Contigs Represented = 13
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:05:16 (hh:mm:ss) Elapsed Time
Round Time: 00:06:53 (hh:mm:ss) Elapsed Time : 13 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 00:00:22 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       299 repeats masked totaling 88812 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10005882 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 10004882 bp
             After Masking: 9605535 bp
             Masked: 3.99 % 
 -- Input Database Coverage: 10005882 bp out of 12726212 bp ( 78.62 % )
Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32131
Comparison Time: 00:05:42 (hh:mm:ss) Elapsed Time, 3111 HSPs Collected
Number of families returned by RECON: 741
Round Time: 00:06:22 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 32726212


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32726212 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       109 repeats masked totaling 20692 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2720127 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 2720127 bp
             After Masking: 2664418 bp
             Masked: 2.05 % 
 -- Input Database Coverage: 12726009 bp out of 12726212 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2415
Comparison Time: 00:01:02 (hh:mm:ss) Elapsed Time, 196 HSPs Collected
Number of families returned by RECON: 97
Round Time: 00:01:10 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 16 families found


Classification Time: 00:00:31 (hh:mm:ss) Elapsed Time


Program Time: 00:14:56 (hh:mm:ss) Elapsed Time