RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.2sOSQd/RM_17012.TueAug130511332024
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: 1723551092
Database = /dev/shm/rModeler.2sOSQd/GCA_014217725.1_ASM1421772v1   - Sequences = 13
  - Bases = 12696838
Storage Throughput = excellent ( 1042.31 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12696678 bp ( 12696678 non ambiguous )
   - Num Contigs Represented = 13
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:07:11 (hh:mm:ss) Elapsed Time
Round Time: 00:08:33 (hh:mm:ss) Elapsed Time : 19 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 00:00:19 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       297 repeats masked totaling 90910 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10001837 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 10001837 bp
             After Masking: 9656566 bp
             Masked: 3.45 % 
 -- Input Database Coverage: 10001837 bp out of 12696838 bp ( 78.77 % )
Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32385
Comparison Time: 00:05:09 (hh:mm:ss) Elapsed Time, 2564 HSPs Collected
Number of families returned by RECON: 756
Round Time: 00:05:36 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 32696838


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32696838 bp
   - Sequence extraction : 00:00:00 (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...
       74 repeats masked totaling 22017 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2694764 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 2694764 bp
             After Masking: 2585721 bp
             Masked: 4.05 % 
 -- Input Database Coverage: 12696601 bp out of 12696838 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2278
Comparison Time: 00:00:51 (hh:mm:ss) Elapsed Time, 170 HSPs Collected
Number of families returned by RECON: 82
Round Time: 00:00:59 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 19 families found


Classification Time: 00:00:28 (hh:mm:ss) Elapsed Time


Program Time: 00:15:36 (hh:mm:ss) Elapsed Time