RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.tKoFrI/RM_959267.FriSep120506582025
Search Engine = rmblast 2.14.1+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1757678818
Database = /dev/shm/rModeler.tKoFrI/GCA_037042035.1_ASM3704203v1 
  - Sequences = 405
  - Bases = 30349585
  - N50 = 315954
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1304284-1397412 |                                                   [ 1 ]
  1211157-1304284 |                                                   [  ]
  1118030-1211157 |                                                   [  ]
  1024903-1118030 |                                                   [  ]
  931776-1024903  |                                                   [ 1 ]
  838648-931775   |                                                   [ 2 ]
  745521-838648   |                                                   [  ]
  652394-745521   |                                                   [ 3 ]
  559267-652394   |                                                   [ 2 ]
  466140-559267   |                                                   [ 3 ]
  373012-466139   |*                                                  [ 7 ]
  279885-373012   |**                                                 [ 14 ]
  186758-279885   |**                                                 [ 18 ]
  93631-186758    |*****                                              [ 37 ]
  504-93631       |************************************************** [ 317 ]

Storage Throughput = excellent ( 1403.67 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 30349526 bp ( 30349215 non ambiguous )
   - Num Contigs Represented = 405
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 164 raw families identified
   - RepeatScout: Running filtering stage.. 162 families remaining
   - RepeatScout: 00:00:54 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 156 families... 00:00:20 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 51 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:19 (hh:mm:ss) Elapsed Time : 105 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...
       1803 repeats masked totaling 530125 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10043224 bp
       Num Contigs Represented = 195
       Non ambiguous bp:
             Initial: 10043056 bp
             After Masking: 9490630 bp
             Masked: 5.50 % 
 -- Input Database Coverage: 10043224 bp out of 30349585 bp ( 33.09 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 60378
Comparison Time: 00:04:36 (hh:mm:ss) Elapsed Time, 4867 HSPs Collected
Number of families returned by RECON: 1663
Round Time: 00:04:57 (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 : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4049 repeats masked totaling 1119499 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 20306251 bp
       Num Contigs Represented = 313
       Non ambiguous bp:
             Initial: 20306108 bp
             After Masking: 19138407 bp
             Masked: 5.75 % 
 -- Input Database Coverage: 30349475 bp out of 30349585 bp ( 100.00 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 248160
Comparison Time: 00:11:28 (hh:mm:ss) Elapsed Time, 19381 HSPs Collected
Number of families returned by RECON: 4396
Round Time: 00:12:14 (hh:mm:ss) Elapsed Time : 12 families discovered.

RepeatScout/RECON discovery complete: 119 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.tKoFrI/RM_959267.FriSep120506582025
# Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib
#   - 18011 proteins
# Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib
#   - 26292 consensus sequences
  - Looking for simple/tandem and low complexity sequences..
  - Looking for similarity to known repeat proteins..
  - Looking for similarity to known repeat consensi..

Classification Time: 00:00:16 (hh:mm:ss) Elapsed Time


Program Time: 00:18:46 (hh:mm:ss) Elapsed Time