RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.QkZ8r1/RM_10196.TueAug130830312024
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: 1723563031
Database = /dev/shm/rModeler.QkZ8r1/GCA_017310615.1_ASM1731061v1   - Sequences = 7
  - Bases = 37996987
Storage Throughput = good ( 894.68 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37996863 bp ( 37996863 non ambiguous )
   - Num Contigs Represented = 7
   - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:14:01 (hh:mm:ss) Elapsed Time
Round Time: 00:33:08 (hh:mm:ss) Elapsed Time : 118 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2248 repeats masked totaling 1603388 bp(s).
   - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10004339 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 10004339 bp
             After Masking: 8372327 bp
             Masked: 16.31 % 
 -- Input Database Coverage: 10004339 bp out of 37996987 bp ( 26.33 % )
Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31125
Comparison Time: 00:05:12 (hh:mm:ss) Elapsed Time, 79872 HSPs Collected
Number of families returned by RECON: 398
Round Time: 01:01:43 (hh:mm:ss) Elapsed Time : 6 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       8283 repeats masked totaling 8131585 bp(s).
   - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27992506 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 27992506 bp
             After Masking: 19740551 bp
             Masked: 29.48 % 
 -- Input Database Coverage: 37996845 bp out of 37996987 bp ( 100.00 % )
Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 248160
Comparison Time: 00:19:03 (hh:mm:ss) Elapsed Time, 12152 HSPs Collected
Number of families returned by RECON: 1680
Round Time: 00:30:38 (hh:mm:ss) Elapsed Time : 18 families discovered.

RepeatScout/RECON discovery complete: 142 families found


Classification Time: 00:18:38 (hh:mm:ss) Elapsed Time


Program Time: 02:24:07 (hh:mm:ss) Elapsed Time