RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.iLrzAp/RM_795.MonAug122131162024
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: 1723523475
Database = /dev/shm/rModeler.iLrzAp/GCA_001700775.1_ASM170077v1   - Sequences = 23
  - Bases = 29805862
Storage Throughput = excellent ( 1060.42 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 29805744 bp ( 29802402 non ambiguous )
   - Num Contigs Represented = 23
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:11:26 (hh:mm:ss) Elapsed Time
Round Time: 00:35:43 (hh:mm:ss) Elapsed Time : 12 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       208 repeats masked totaling 145144 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10032147 bp
       Num Contigs Represented = 22
       Non ambiguous bp:
             Initial: 10030729 bp
             After Masking: 9823153 bp
             Masked: 2.07 % 
 -- Input Database Coverage: 10032147 bp out of 29805862 bp ( 33.66 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32896
Comparison Time: 00:04:37 (hh:mm:ss) Elapsed Time, 1169 HSPs Collected
Number of families returned by RECON: 550
Round Time: 00:05:28 (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 00:00:22 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       360 repeats masked totaling 223793 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 19773564 bp
       Num Contigs Represented = 20
       Non ambiguous bp:
             Initial: 19771640 bp
             After Masking: 19420307 bp
             Masked: 1.78 % 
 -- Input Database Coverage: 29805711 bp out of 29805862 bp ( 100.00 % )
Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 126253
Comparison Time: 00:13:43 (hh:mm:ss) Elapsed Time, 3934 HSPs Collected
Number of families returned by RECON: 1581
Round Time: 00:15:17 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 16 families found


Classification Time: 00:01:36 (hh:mm:ss) Elapsed Time


Program Time: 00:58:04 (hh:mm:ss) Elapsed Time