RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.N0NAwC/RM_10882.TueAug130342482024
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: 1723545767
Database = /dev/shm/rModeler.N0NAwC/GCA_008728235.1_ASM872823v1   - Sequences = 10
  - Bases = 31885420
Storage Throughput = excellent ( 1052.69 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 31885277 bp ( 31885277 non ambiguous )
   - Num Contigs Represented = 10
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:15:21 (hh:mm:ss) Elapsed Time
Round Time: 00:19:13 (hh:mm:ss) Elapsed Time : 153 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2244 repeats masked totaling 872145 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10012842 bp
       Num Contigs Represented = 10
       Non ambiguous bp:
             Initial: 10012842 bp
             After Masking: 9092873 bp
             Masked: 9.19 % 
 -- Input Database Coverage: 10012842 bp out of 31885420 bp ( 31.40 % )
Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31375
Comparison Time: 00:05:22 (hh:mm:ss) Elapsed Time, 8229 HSPs Collected
Number of families returned by RECON: 1536
Round Time: 00:07:26 (hh:mm:ss) Elapsed Time : 4 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4607 repeats masked totaling 1870603 bp(s).
   - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 21872364 bp
       Num Contigs Represented = 10
       Non ambiguous bp:
             Initial: 21872364 bp
             After Masking: 19900559 bp
             Masked: 9.02 % 
 -- Input Database Coverage: 31885206 bp out of 31885420 bp ( 100.00 % )
Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 151525
Comparison Time: 00:19:21 (hh:mm:ss) Elapsed Time, 17465 HSPs Collected
Number of families returned by RECON: 4504
Round Time: 00:21:02 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 165 families found


Classification Time: 00:10:24 (hh:mm:ss) Elapsed Time


Program Time: 00:58:05 (hh:mm:ss) Elapsed Time