RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.ENjImX/RM_3361509.WedSep101436592025
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: 1757540219
Database = /dev/shm/rModeler.ENjImX/GCA_018154895.1_ASM1815489v1 
  - Sequences = 347
  - Bases = 19536456
  - N50 = 580121
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1593389-1707189 |                                                   [ 1 ]
  1479590-1593389 |                                                   [  ]
  1365791-1479590 |                                                   [  ]
  1251991-1365790 |                                                   [  ]
  1138192-1251991 |                                                   [  ]
  1024393-1138192 |                                                   [ 2 ]
  910594-1024393  |                                                   [ 2 ]
  796794-910593   |                                                   [ 1 ]
  682995-796794   |                                                   [ 1 ]
  569196-682995   |                                                   [ 3 ]
  455397-569196   |*                                                  [ 7 ]
  341597-455396   |                                                   [ 5 ]
  227798-341597   |*                                                  [ 8 ]
  113999-227798   |*                                                  [ 10 ]
  200-113999      |************************************************** [ 307 ]

Storage Throughput = excellent ( 1633.13 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19536301 bp ( 19531090 non ambiguous )
   - Num Contigs Represented = 347
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 22 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:00:26 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 21 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:34 (hh:mm:ss) Elapsed Time : 18 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       331 repeats masked totaling 62562 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10007801 bp
       Num Contigs Represented = 186
       Non ambiguous bp:
             Initial: 10004996 bp
             After Masking: 9888028 bp
             Masked: 1.17 % 
 -- Input Database Coverage: 10007801 bp out of 19536456 bp ( 51.23 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 79800
Comparison Time: 00:04:40 (hh:mm:ss) Elapsed Time, 19686 HSPs Collected
Number of families returned by RECON: 1579
Round Time: 00:05:12 (hh:mm:ss) Elapsed Time : 6 families discovered.
   - Increasing sample size to include end piece now = 39536456


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39536456 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...
       2618 repeats masked totaling 282338 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9528495 bp
       Num Contigs Represented = 208
       Non ambiguous bp:
             Initial: 9526089 bp
             After Masking: 9190153 bp
             Masked: 3.53 % 
 -- Input Database Coverage: 19536296 bp out of 19536456 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 80200
Comparison Time: 00:04:26 (hh:mm:ss) Elapsed Time, 2218 HSPs Collected
Number of families returned by RECON: 712
Round Time: 00:04:41 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.ENjImX/RM_3361509.WedSep101436592025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:10:33 (hh:mm:ss) Elapsed Time