RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.KohJvY/RM_27673.TueAug130319592024
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: 1723544398
Database = /dev/shm/rModeler.KohJvY/GCA_008080495.1_ASM808049v1   - Sequences = 7
  - Bases = 33618380
Storage Throughput = excellent ( 1039.07 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 33618231 bp ( 33618231 non ambiguous )
   - Num Contigs Represented = 7
   - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:13:23 (hh:mm:ss) Elapsed Time
Round Time: 07:04:51 (hh:mm:ss) Elapsed Time : 57 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 00:00:25 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1010 repeats masked totaling 1038166 bp(s).
   - TE Masking time 00:02:58 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10035581 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 10035581 bp
             After Masking: 8938952 bp
             Masked: 10.93 % 
 -- Input Database Coverage: 10035581 bp out of 33618380 bp ( 29.85 % )
Sampling Time: 00:03:27 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31375
Comparison Time: 00:07:19 (hh:mm:ss) Elapsed Time, 2185 HSPs Collected
Number of families returned by RECON: 574
Round Time: 00:34:31 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2273 repeats masked totaling 2477627 bp(s).
   - TE Masking time 00:07:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 23582635 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 23582635 bp
             After Masking: 20983807 bp
             Masked: 11.02 % 
 -- Input Database Coverage: 33618216 bp out of 33618380 bp ( 100.00 % )
Sampling Time: 00:08:14 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 176121
Comparison Time: 00:22:31 (hh:mm:ss) Elapsed Time, 8907 HSPs Collected
Number of families returned by RECON: 1968
Round Time: 00:41:36 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 67 families found


Classification Time: 00:08:05 (hh:mm:ss) Elapsed Time


Program Time: 08:29:03 (hh:mm:ss) Elapsed Time