RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.lbnKQi/RM_23930.TueAug131450472024
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: 1723585846
Database = /dev/shm/rModeler.lbnKQi/GCA_900237765.1_BghRACE1_v1   - Sequences = 99
  - Bases = 116475897
Storage Throughput = good ( 973.69 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40026548 bp ( 40026548 non ambiguous )
   - Num Contigs Represented = 75
   - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:11:29 (hh:mm:ss) Elapsed Time
Round Time: 00:38:36 (hh:mm:ss) Elapsed Time : 598 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       13568 repeats masked totaling 7295864 bp(s).
   - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10004808 bp
       Num Contigs Represented = 52
       Non ambiguous bp:
             Initial: 10004808 bp
             After Masking: 2678358 bp
             Masked: 73.23 % 
 -- Input Database Coverage: 10004808 bp out of 116475897 bp ( 8.59 % )
Sampling Time: 00:00:53 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32131
Comparison Time: 00:03:43 (hh:mm:ss) Elapsed Time, 6359 HSPs Collected
Number of families returned by RECON: 338
Round Time: 00:05:09 (hh:mm:ss) Elapsed Time : 12 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       40879 repeats masked totaling 22553126 bp(s).
   - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30021660 bp
       Num Contigs Represented = 72
       Non ambiguous bp:
             Initial: 30021660 bp
             After Masking: 7398253 bp
             Masked: 75.36 % 
 -- Input Database Coverage: 40026468 bp out of 116475897 bp ( 34.36 % )
Sampling Time: 00:03:38 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 289941
Comparison Time: 00:14:29 (hh:mm:ss) Elapsed Time, 20165 HSPs Collected
Number of families returned by RECON: 1004
Round Time: 00:18:49 (hh:mm:ss) Elapsed Time : 40 families discovered.


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 90000000 bp
   - Sequence extraction : 00:00:11 (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...
       107945 repeats masked totaling 58081855 bp(s).
   - TE Masking time 00:04:49 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 76449280 bp
       Num Contigs Represented = 95
       Non ambiguous bp:
             Initial: 76449280 bp
             After Masking: 18180508 bp
             Masked: 76.22 % 
 -- Input Database Coverage: 116475748 bp out of 116475897 bp ( 100.00 % )
Sampling Time: 00:06:27 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1892485
Comparison Time: 00:53:31 (hh:mm:ss) Elapsed Time, 60233 HSPs Collected
Number of families returned by RECON: 2467
Round Time: 01:01:24 (hh:mm:ss) Elapsed Time : 141 families discovered.

RepeatScout/RECON discovery complete: 791 families found


Classification Time: 01:29:42 (hh:mm:ss) Elapsed Time


Program Time: 03:33:40 (hh:mm:ss) Elapsed Time