RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.68XIG7/RM_29099.MonAug121220132024
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: 1723490412
Database = /dev/shm/rModeler.68XIG7/GCA_000002545.2_ASM254v2   - Sequences = 13
  - Bases = 12318245
Storage Throughput = excellent ( 1055.87 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12318146 bp ( 12317846 non ambiguous )
   - Num Contigs Represented = 13
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:07:12 (hh:mm:ss) Elapsed Time
Round Time: 00:09:28 (hh:mm:ss) Elapsed Time : 8 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 00:00:16 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       212 repeats masked totaling 42527 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10035567 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 10035267 bp
             After Masking: 9891455 bp
             Masked: 1.43 % 
 -- Input Database Coverage: 10035567 bp out of 12318245 bp ( 81.47 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32640
Comparison Time: 00:05:47 (hh:mm:ss) Elapsed Time, 3319 HSPs Collected
Number of families returned by RECON: 802
Round Time: 00:06:15 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 32318245


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32318245 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       18 repeats masked totaling 3114 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2282499 bp
       Num Contigs Represented = 12
       Non ambiguous bp:
             Initial: 2282499 bp
             After Masking: 2268956 bp
             Masked: 0.59 % 
 -- Input Database Coverage: 12318066 bp out of 12318245 bp ( 100.00 % )
Sampling Time: 00:00:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1711
Comparison Time: 00:00:42 (hh:mm:ss) Elapsed Time, 99 HSPs Collected
Number of families returned by RECON: 63
Round Time: 00:00:48 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 9 families found


Classification Time: 00:00:11 (hh:mm:ss) Elapsed Time


Program Time: 00:16:42 (hh:mm:ss) Elapsed Time