RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.rn9p2r/RM_18802.ThuSep121125552024
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: 1726165554
Database = /dev/shm/rModeler.rn9p2r/GCA_900002395.1_PYYM01   - Sequences = 197
  - Bases = 22031682
  - N50 = 1783079
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2463235-2639166 |                                                   [ 2 ]
  2287305-2463235 |                                                   [  ]
  2111375-2287305 |                                                   [  ]
  1935445-2111375 |                                                   [  ]
  1759515-1935445 |*                                                  [ 4 ]
  1583585-1759515 |                                                   [  ]
  1407655-1583585 |                                                   [ 1 ]
  1231725-1407655 |                                                   [  ]
  1055795-1231725 |                                                   [  ]
  879865-1055795  |*                                                  [ 4 ]
  703935-879865   |                                                   [ 2 ]
  528005-703935   |                                                   [ 1 ]
  352075-528005   |                                                   [  ]
  176145-352075   |                                                   [  ]
  215-176145      |************************************************** [ 183 ]

Storage Throughput = excellent ( 1126.59 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22031678 bp ( 21430031 non ambiguous )
   - Num Contigs Represented = 197
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:09:38 (hh:mm:ss) Elapsed Time
Round Time: 00:38:05 (hh:mm:ss) Elapsed Time : 57 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 00:01:42 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2636 repeats masked totaling 1306065 bp(s).
   - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10254355 bp
       Num Contigs Represented = 104
       Non ambiguous bp:
             Initial: 10013674 bp
             After Masking: 8370987 bp
             Masked: 16.40 % 
 -- Input Database Coverage: 10254355 bp out of 22031682 bp ( 46.54 % )
Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 54946
Comparison Time: 01:04:39 (hh:mm:ss) Elapsed Time, 42218 HSPs Collected
Number of families returned by RECON: 285
Round Time: 01:08:59 (hh:mm:ss) Elapsed Time : 10 families discovered.
   - Increasing sample size to include end piece now = 42031682


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42031682 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:58 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3969 repeats masked totaling 1797748 bp(s).
   - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 11777313 bp
       Num Contigs Represented = 112
       Non ambiguous bp:
             Initial: 11416347 bp
             After Masking: 9213709 bp
             Masked: 19.29 % 
 -- Input Database Coverage: 22031668 bp out of 22031682 bp ( 100.00 % )
Sampling Time: 00:02:42 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 70876
Comparison Time: 01:34:59 (hh:mm:ss) Elapsed Time, 1356 HSPs Collected
Number of families returned by RECON: 324
Round Time: 01:37:48 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 68 families found


Classification Time: 00:03:30 (hh:mm:ss) Elapsed Time


Program Time: 03:28:22 (hh:mm:ss) Elapsed Time