RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.o0lI3z/RM_2398.ThuSep121228352024
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: 1726169314
Database = /dev/shm/rModeler.o0lI3z/GCA_016097395.1_Ncaninum_LIV   - Sequences = 44
  - Bases = 61494165
Storage Throughput = excellent ( 1176.65 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40008455 bp ( 40008455 non ambiguous )
   - Num Contigs Represented = 36
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:11:29 (hh:mm:ss) Elapsed Time
Round Time: 00:13:32 (hh:mm:ss) Elapsed Time : 138 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 00:00:27 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1380 repeats masked totaling 360142 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10009550 bp
       Num Contigs Represented = 19
       Non ambiguous bp:
             Initial: 10009550 bp
             After Masking: 9482289 bp
             Masked: 5.27 % 
 -- Input Database Coverage: 10009550 bp out of 61494165 bp ( 16.28 % )
Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32131
Comparison Time: 00:05:05 (hh:mm:ss) Elapsed Time, 9772 HSPs Collected
Number of families returned by RECON: 917
Round Time: 00:05:56 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5276 repeats masked totaling 1437405 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30038905 bp
       Num Contigs Represented = 31
       Non ambiguous bp:
             Initial: 30038905 bp
             After Masking: 28119856 bp
             Masked: 6.39 % 
 -- Input Database Coverage: 40048455 bp out of 61494165 bp ( 65.13 % )
Sampling Time: 00:01:32 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 290703
Comparison Time: 00:24:35 (hh:mm:ss) Elapsed Time, 78675 HSPs Collected
Number of families returned by RECON: 4039
Round Time: 00:28:03 (hh:mm:ss) Elapsed Time : 11 families discovered.
   - Increasing sample size to include end piece now = 111484615


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 111484615 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4031 repeats masked totaling 1059369 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 21445501 bp
       Num Contigs Represented = 23
       Non ambiguous bp:
             Initial: 21445501 bp
             After Masking: 20006566 bp
             Masked: 6.71 % 
 -- Input Database Coverage: 61493956 bp out of 61494165 bp ( 100.00 % )
Sampling Time: 00:00:59 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 147153
Comparison Time: 00:13:51 (hh:mm:ss) Elapsed Time, 32452 HSPs Collected
Number of families returned by RECON: 2334
Round Time: 00:15:48 (hh:mm:ss) Elapsed Time : 6 families discovered.

RepeatScout/RECON discovery complete: 157 families found


Classification Time: 00:03:48 (hh:mm:ss) Elapsed Time


Program Time: 01:07:07 (hh:mm:ss) Elapsed Time