RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.Q9ohFy/RM_1689612.WedAug201520222025
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: 1755728421
Database = /dev/shm/rModeler.Q9ohFy/GCA_002759435.2_Cand_auris_B8441_V2   - Sequences = 15
  - Bases = 12365959
Storage Throughput = excellent ( 1608.76 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12365822 bp ( 12365522 non ambiguous )
   - Num Contigs Represented = 15
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:02:21 (hh:mm:ss) Elapsed Time
Round Time: 00:02:31 (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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       147 repeats masked totaling 18170 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10037056 bp
       Num Contigs Represented = 14
       Non ambiguous bp:
             Initial: 10036756 bp
             After Masking: 9994541 bp
             Masked: 0.42 % 
 -- Input Database Coverage: 10037056 bp out of 12365959 bp ( 81.17 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33153
Comparison Time: 00:03:14 (hh:mm:ss) Elapsed Time, 3019 HSPs Collected
Number of families returned by RECON: 799
Round Time: 00:04:00 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 32365959


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32365959 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       31 repeats masked totaling 3646 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2328698 bp
       Num Contigs Represented = 11
       Non ambiguous bp:
             Initial: 2328698 bp
             After Masking: 2314072 bp
             Masked: 0.63 % 
 -- Input Database Coverage: 12365754 bp out of 12365959 bp ( 100.00 % )
Sampling Time: 00:00:03 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1770
Comparison Time: 00:00:32 (hh:mm:ss) Elapsed Time, 123 HSPs Collected
Number of families returned by RECON: 80
Round Time: 00:00:35 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 7 families found


Classification Time: 00:00:11 (hh:mm:ss) Elapsed Time


Program Time: 00:07:17 (hh:mm:ss) Elapsed Time