RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.5O6Cdd/RM_26752.ThuSep121019442024
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: 1726161584
Database = /dev/shm/rModeler.5O6Cdd/GCA_900162085.1_PkA1H1_v1   - Sequences = 16
  - Bases = 24311210
Storage Throughput = excellent ( 1124.68 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 24311152 bp ( 24162897 non ambiguous )
   - Num Contigs Represented = 16
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:11:08 (hh:mm:ss) Elapsed Time
Round Time: 00:22:05 (hh:mm:ss) Elapsed Time : 104 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 00:01:33 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3494 repeats masked totaling 473741 bp(s).
   - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10050902 bp
       Num Contigs Represented = 16
       Non ambiguous bp:
             Initial: 10010924 bp
             After Masking: 8779923 bp
             Masked: 12.30 % 
 -- Input Database Coverage: 10050902 bp out of 24311210 bp ( 41.34 % )
Sampling Time: 00:01:53 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32385
Comparison Time: 00:36:20 (hh:mm:ss) Elapsed Time, 19304 HSPs Collected
Number of families returned by RECON: 1587
Round Time: 00:38:57 (hh:mm:ss) Elapsed Time : 17 families discovered.
   - Increasing sample size to include end piece now = 44311210


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 44311210 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:02:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5807 repeats masked totaling 882957 bp(s).
   - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 14260229 bp
       Num Contigs Represented = 14
       Non ambiguous bp:
             Initial: 14151952 bp
             After Masking: 12215326 bp
             Masked: 13.68 % 
 -- Input Database Coverage: 24311131 bp out of 24311210 bp ( 100.00 % )
Sampling Time: 00:02:57 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 65341
Comparison Time: 01:01:39 (hh:mm:ss) Elapsed Time, 14911 HSPs Collected
Number of families returned by RECON: 2416
Round Time: 01:05:25 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 129 families found


Classification Time: 00:03:53 (hh:mm:ss) Elapsed Time


Program Time: 02:10:20 (hh:mm:ss) Elapsed Time