RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.WPwIWK/RM_16714.TueAug131015132024
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: 1723569313
Database = /dev/shm/rModeler.WPwIWK/GCA_017607445.1_ASM1760744v1   - Sequences = 12
  - Bases = 39447273
Storage Throughput = good ( 954.85 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39447143 bp ( 39447143 non ambiguous )
   - Num Contigs Represented = 12
   - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:15:53 (hh:mm:ss) Elapsed Time
Round Time: 00:45:06 (hh:mm:ss) Elapsed Time : 78 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 00:00:22 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3326 repeats masked totaling 2838284 bp(s).
   - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10001972 bp
       Num Contigs Represented = 9
       Non ambiguous bp:
             Initial: 10001972 bp
             After Masking: 7054497 bp
             Masked: 29.47 % 
 -- Input Database Coverage: 10001972 bp out of 39447273 bp ( 25.36 % )
Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31878
Comparison Time: 00:04:34 (hh:mm:ss) Elapsed Time, 74902 HSPs Collected
Number of families returned by RECON: 312
Round Time: 00:09:39 (hh:mm:ss) Elapsed Time : 10 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 00:01:01 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       11646 repeats masked totaling 9536024 bp(s).
   - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29445091 bp
       Num Contigs Represented = 12
       Non ambiguous bp:
             Initial: 29445091 bp
             After Masking: 19608846 bp
             Masked: 33.41 % 
 -- Input Database Coverage: 39447063 bp out of 39447273 bp ( 100.00 % )
Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 274170
Comparison Time: 00:21:54 (hh:mm:ss) Elapsed Time, 8322 HSPs Collected
Number of families returned by RECON: 1694
Round Time: 00:24:06 (hh:mm:ss) Elapsed Time : 17 families discovered.

RepeatScout/RECON discovery complete: 105 families found


Classification Time: 00:10:50 (hh:mm:ss) Elapsed Time


Program Time: 01:29:41 (hh:mm:ss) Elapsed Time