RepeatModeler Version 2.0.4
===========================
Using output directory = /scratch/tmp/rModeler.0bjjE6/RM_2035725.SatNov161512112024
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: 1731798731
Database = /scratch/tmp/rModeler.0bjjE6/GCF_000002845.2_ASM284v2   - Sequences = 138
  - Bases = 32068771
  - N50 = 1157752
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2507596-2686643 |                                                   [ 1 ]
  2328550-2507596 |                                                   [  ]
  2149504-2328550 |                                                   [  ]
  1970457-2149503 |                                                   [ 1 ]
  1791411-1970457 |                                                   [  ]
  1612365-1791411 |                                                   [ 1 ]
  1433318-1612364 |*                                                  [ 3 ]
  1254272-1433318 |                                                   [ 1 ]
  1075226-1254272 |*                                                  [ 3 ]
  896179-1075225  |                                                   [ 1 ]
  717133-896179   |*                                                  [ 4 ]
  538087-717133   |******                                             [ 13 ]
  359040-538086   |**                                                 [ 6 ]
  179994-359040   |                                                   [ 2 ]
  948-179994      |************************************************** [ 102 ]

Storage Throughput = excellent ( 1471.40 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 32068637 bp ( 31986758 non ambiguous )
   - Num Contigs Represented = 138
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:05:20 (hh:mm:ss) Elapsed Time
Round Time: 00:07:06 (hh:mm:ss) Elapsed Time : 151 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 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2015 repeats masked totaling 611189 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10030596 bp
       Num Contigs Represented = 75
       Non ambiguous bp:
             Initial: 10002923 bp
             After Masking: 9256753 bp
             Masked: 7.46 % 
 -- Input Database Coverage: 10030596 bp out of 32068771 bp ( 31.28 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 41041
Comparison Time: 00:03:23 (hh:mm:ss) Elapsed Time, 2333 HSPs Collected
Number of families returned by RECON: 917
Round Time: 00:03:43 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4513 repeats masked totaling 1386999 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 22038023 bp
       Num Contigs Represented = 100
       Non ambiguous bp:
             Initial: 21983817 bp
             After Masking: 20293072 bp
             Masked: 7.69 % 
 -- Input Database Coverage: 32068619 bp out of 32068771 bp ( 100.00 % )
Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 190036
Comparison Time: 00:10:28 (hh:mm:ss) Elapsed Time, 11297 HSPs Collected
Number of families returned by RECON: 2959
Round Time: 00:11:16 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 160 families found


Classification Time: 00:02:40 (hh:mm:ss) Elapsed Time


Program Time: 00:24:45 (hh:mm:ss) Elapsed Time