RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.thDAu1/RM_32538.MonAug121706022024
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: 1723507562
Database = /dev/shm/rModeler.thDAu1/GCA_000723665.1_454Minimus   - Sequences = 209
  - Bases = 33531723
  - N50 = 385448
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1226195-1313670 |                                                   [ 2 ]
  1138721-1226195 |                                                   [ 1 ]
  1051247-1138721 |                                                   [  ]
  963773-1051247  |                                                   [ 1 ]
  876299-963773   |                                                   [ 1 ]
  788825-876299   |                                                   [ 2 ]
  701351-788825   |                                                   [ 1 ]
  613876-701350   |*                                                  [ 4 ]
  526402-613876   |*                                                  [ 4 ]
  438928-526402   |                                                   [ 1 ]
  351454-438928   |*****                                              [ 13 ]
  263980-351454   |*****                                              [ 13 ]
  176506-263980   |********                                           [ 22 ]
  89032-176506    |********                                           [ 20 ]
  1558-89032      |************************************************** [ 124 ]

Storage Throughput = excellent ( 1064.00 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 33531609 bp ( 30977187 non ambiguous )
   - Num Contigs Represented = 209
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:13:53 (hh:mm:ss) Elapsed Time
Round Time: 00:18:53 (hh:mm:ss) Elapsed Time : 153 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 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3410 repeats masked totaling 1063481 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10971252 bp
       Num Contigs Represented = 118
       Non ambiguous bp:
             Initial: 10013899 bp
             After Masking: 8925406 bp
             Masked: 10.87 % 
 -- Input Database Coverage: 10971252 bp out of 33531723 bp ( 32.72 % )
Sampling Time: 00:00:23 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 47586
Comparison Time: 00:05:44 (hh:mm:ss) Elapsed Time, 3846 HSPs Collected
Number of families returned by RECON: 1453
Round Time: 00:06:17 (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 00:00:26 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6675 repeats masked totaling 2098151 bp(s).
   - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 22560283 bp
       Num Contigs Represented = 175
       Non ambiguous bp:
             Initial: 20963214 bp
             After Masking: 18795378 bp
             Masked: 10.34 % 
 -- Input Database Coverage: 33531535 bp out of 33531723 bp ( 100.00 % )
Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 213531
Comparison Time: 00:19:15 (hh:mm:ss) Elapsed Time, 17943 HSPs Collected
Number of families returned by RECON: 4410
Round Time: 00:25:20 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 163 families found


Classification Time: 00:06:50 (hh:mm:ss) Elapsed Time


Program Time: 00:57:20 (hh:mm:ss) Elapsed Time