RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.jk6FFh/RM_28455.WedSep181042232024
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: 1726681343
Database = /dev/shm/rModeler.jk6FFh/GCA_002759435.3_Cand_auris_B8441_V3   - Sequences = 7
  - Bases = 12406600
Storage Throughput = excellent ( 1116.34 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12406522 bp ( 12406322 non ambiguous )
   - Num Contigs Represented = 7
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:06:33 (hh:mm:ss) Elapsed Time
Round Time: 00:06:55 (hh:mm:ss) Elapsed Time : 5 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 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       136 repeats masked totaling 17787 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10036988 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 10036788 bp
             After Masking: 9985911 bp
             Masked: 0.51 % 
 -- Input Database Coverage: 10036988 bp out of 12406600 bp ( 80.90 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32385
Comparison Time: 00:05:50 (hh:mm:ss) Elapsed Time, 2824 HSPs Collected
Number of families returned by RECON: 801
Round Time: 00:11:33 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 32406600


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32406600 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       44 repeats masked totaling 6062 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2369486 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 2369486 bp
             After Masking: 2356627 bp
             Masked: 0.54 % 
 -- Input Database Coverage: 12406474 bp out of 12406600 bp ( 100.00 % )
Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1770
Comparison Time: 00:00:47 (hh:mm:ss) Elapsed Time, 169 HSPs Collected
Number of families returned by RECON: 84
Round Time: 00:00:54 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 6 families found


Classification Time: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:19:30 (hh:mm:ss) Elapsed Time