RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.cqCeYi/RM_3315.MonAug122358012024
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: 1723532280
Database = /dev/shm/rModeler.cqCeYi/GCA_002775015.1_Cand_auris_B11221_V1   - Sequences = 20
  - Bases = 12741178
Storage Throughput = excellent ( 1060.32 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12741068 bp ( 12740768 non ambiguous )
   - Num Contigs Represented = 20
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:06:47 (hh:mm:ss) Elapsed Time
Round Time: 00:07:08 (hh:mm:ss) Elapsed Time : 7 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...
       161 repeats masked totaling 20403 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10007891 bp
       Num Contigs Represented = 18
       Non ambiguous bp:
             Initial: 10007691 bp
             After Masking: 9960951 bp
             Masked: 0.47 % 
 -- Input Database Coverage: 10007891 bp out of 12741178 bp ( 78.55 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32896
Comparison Time: 00:05:47 (hh:mm:ss) Elapsed Time, 3045 HSPs Collected
Number of families returned by RECON: 730
Round Time: 00:06:10 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 32741178


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32741178 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...
       52 repeats masked totaling 7125 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2733097 bp
       Num Contigs Represented = 9
       Non ambiguous bp:
             Initial: 2732997 bp
             After Masking: 2718289 bp
             Masked: 0.54 % 
 -- Input Database Coverage: 12740988 bp out of 12741178 bp ( 100.00 % )
Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2415
Comparison Time: 00:00:58 (hh:mm:ss) Elapsed Time, 198 HSPs Collected
Number of families returned by RECON: 102
Round Time: 00:01:04 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 8 families found


Classification Time: 00:00:14 (hh:mm:ss) Elapsed Time


Program Time: 00:14:36 (hh:mm:ss) Elapsed Time