RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.0Zbons/RM_10654.SunJul71613462024
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: 1720394026
Database = /dev/shm/rModeler.0Zbons/GCF_029203305.1_ASM2920330v1   - Sequences = 8
  - Bases = 10858197
Storage Throughput = excellent ( 1047.64 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 10858110 bp ( 10858110 non ambiguous )
   - Num Contigs Represented = 8
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:05:41 (hh:mm:ss) Elapsed Time
Round Time: 00:07:33 (hh:mm:ss) Elapsed Time : 10 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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       331 repeats masked totaling 120294 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10012090 bp
       Num Contigs Represented = 8
       Non ambiguous bp:
             Initial: 10012090 bp
             After Masking: 9794554 bp
             Masked: 2.17 % 
 -- Input Database Coverage: 10012090 bp out of 10858197 bp ( 92.21 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32385
Comparison Time: 00:04:50 (hh:mm:ss) Elapsed Time, 4276 HSPs Collected
Number of families returned by RECON: 895
Round Time: 00:05:16 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 30858197


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30858197 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       20 repeats masked totaling 3550 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 846014 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 846014 bp
             After Masking: 838300 bp
             Masked: 0.91 % 
 -- Input Database Coverage: 10858104 bp out of 10858197 bp ( 100.00 % )
Sampling Time: 00:00:03 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 210
Comparison Time: 00:00:14 (hh:mm:ss) Elapsed Time, 15 HSPs Collected
Round Time: 00:00:17 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 13 families found


Classification Time: 00:00:33 (hh:mm:ss) Elapsed Time


Program Time: 00:13:39 (hh:mm:ss) Elapsed Time