RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.s81Ajy/RM_1956.ThuSep120814222024
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: 1726154061
Database = /dev/shm/rModeler.s81Ajy/GCA_903994265.1_PVSEL_v1   - Sequences = 16
  - Bases = 19533052
Storage Throughput = excellent ( 1210.36 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19532903 bp ( 19531803 non ambiguous )
   - Num Contigs Represented = 16
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:09:17 (hh:mm:ss) Elapsed Time
Round Time: 00:31:09 (hh:mm:ss) Elapsed Time : 54 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 00:01:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1664 repeats masked totaling 839995 bp(s).
   - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10020088 bp
       Num Contigs Represented = 15
       Non ambiguous bp:
             Initial: 10019488 bp
             After Masking: 9088494 bp
             Masked: 9.29 % 
 -- Input Database Coverage: 10020088 bp out of 19533052 bp ( 51.30 % )
Sampling Time: 00:01:44 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31878
Comparison Time: 00:55:41 (hh:mm:ss) Elapsed Time, 8538 HSPs Collected
Number of families returned by RECON: 165
Round Time: 00:58:57 (hh:mm:ss) Elapsed Time : 9 families discovered.
   - Increasing sample size to include end piece now = 39533052


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39533052 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1934 repeats masked totaling 1104990 bp(s).
   - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9512735 bp
       Num Contigs Represented = 15
       Non ambiguous bp:
             Initial: 9512235 bp
             After Masking: 8303392 bp
             Masked: 12.71 % 
 -- Input Database Coverage: 19532823 bp out of 19533052 bp ( 100.00 % )
Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 29403
Comparison Time: 00:29:49 (hh:mm:ss) Elapsed Time, 772 HSPs Collected
Number of families returned by RECON: 204
Round Time: 00:31:32 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 63 families found


Classification Time: 00:03:36 (hh:mm:ss) Elapsed Time


Program Time: 02:05:14 (hh:mm:ss) Elapsed Time