RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.yxJl9Q/RM_2984408.WedSep102004302025
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: 1757559870
Database = /dev/shm/rModeler.yxJl9Q/GCA_020284045.1_ASM2028404v1 
  - Sequences = 302
  - Bases = 35112258
  - N50 = 1039065
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2795888-2995523 |                                                   [ 1 ]
  2596254-2795888 |                                                   [  ]
  2396619-2596253 |                                                   [  ]
  2196985-2396619 |                                                   [  ]
  1997350-2196984 |                                                   [ 1 ]
  1797716-1997350 |                                                   [ 1 ]
  1598081-1797715 |                                                   [  ]
  1398447-1598081 |                                                   [ 4 ]
  1198812-1398446 |                                                   [ 2 ]
  999178-1198812  |                                                   [ 1 ]
  799543-999177   |                                                   [ 1 ]
  599909-799543   |**                                                 [ 12 ]
  400274-599908   |                                                   [ 5 ]
  200640-400274   |**                                                 [ 15 ]
  1006-200640     |************************************************** [ 259 ]

Storage Throughput = excellent ( 1608.21 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 35112216 bp ( 35095095 non ambiguous )
   - Num Contigs Represented = 302
   - 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.. : 70 raw families identified
   - RepeatScout: Running filtering stage.. 46 families remaining
   - RepeatScout: 00:00:36 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 45 families... 00:01:23 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 7 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:02:04 (hh:mm:ss) Elapsed Time : 38 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...
       297 repeats masked totaling 107434 bp(s).
   - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10015105 bp
       Num Contigs Represented = 116
       Non ambiguous bp:
             Initial: 10010329 bp
             After Masking: 9890476 bp
             Masked: 1.20 % 
 -- Input Database Coverage: 10015105 bp out of 35112258 bp ( 28.52 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 49770
Comparison Time: 00:04:51 (hh:mm:ss) Elapsed Time, 2128 HSPs Collected
Number of families returned by RECON: 845
Round Time: 00:05:13 (hh:mm:ss) Elapsed Time : 0 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 00:00:16 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       828 repeats masked totaling 320616 bp(s).
   - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 25097040 bp
       Num Contigs Represented = 233
       Non ambiguous bp:
             Initial: 25084695 bp
             After Masking: 24738754 bp
             Masked: 1.38 % 
 -- Input Database Coverage: 35112145 bp out of 35112258 bp ( 100.00 % )
Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 316410
Comparison Time: 00:23:36 (hh:mm:ss) Elapsed Time, 13726 HSPs Collected
Number of families returned by RECON: 3194
Round Time: 02:00:18 (hh:mm:ss) Elapsed Time : 5 families discovered.

RepeatScout/RECON discovery complete: 43 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.yxJl9Q/RM_2984408.WedSep102004302025
# 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: 00:00:17 (hh:mm:ss) Elapsed Time


Program Time: 02:07:52 (hh:mm:ss) Elapsed Time