RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.7Ti7uG/RM_3347510.ThuFeb120649082026
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: 1770907748
Database = /dev/shm/rModeler.7Ti7uG/GCA_027924045.1_AbraIFM66950_1.0 
  - Sequences = 2291
  - Bases = 36041292
  - N50 = 45534
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  231114-247587 |                                                   [ 1 ]
  214642-231114 |                                                   [  ]
  198169-214641 |                                                   [ 1 ]
  181697-198169 |                                                   [ 1 ]
  165224-181696 |                                                   [  ]
  148752-165224 |                                                   [ 2 ]
  132279-148751 |                                                   [ 7 ]
  115807-132279 |                                                   [ 15 ]
  99334-115806  |                                                   [ 10 ]
  82862-99334   |                                                   [ 31 ]
  66389-82861   |*                                                  [ 52 ]
  49917-66389   |**                                                 [ 91 ]
  33444-49916   |****                                               [ 139 ]
  16972-33444   |********                                           [ 279 ]
  500-16972     |************************************************** [ 1662 ]

Storage Throughput = excellent ( 1642.79 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36041244 bp ( 35954231 non ambiguous )
   - Num Contigs Represented = 2291
   - 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.. : 19 raw families identified
   - RepeatScout: Running filtering stage.. 14 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 13 families... 00:00:03 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:45 (hh:mm:ss) Elapsed Time : 13 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       181 repeats masked totaling 33804 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10048447 bp
       Num Contigs Represented = 706
       Non ambiguous bp:
             Initial: 10027039 bp
             After Masking: 9970057 bp
             Masked: 0.57 % 
 -- Input Database Coverage: 10048447 bp out of 36041292 bp ( 27.88 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 272691
Comparison Time: 00:04:39 (hh:mm:ss) Elapsed Time, 1768 HSPs Collected
Number of families returned by RECON: 804
Round Time: 00:04:48 (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 00:00:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       460 repeats masked totaling 85781 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 25992793 bp
       Num Contigs Represented = 1715
       Non ambiguous bp:
             Initial: 25927188 bp
             After Masking: 25787729 bp
             Masked: 0.54 % 
 -- Input Database Coverage: 36041240 bp out of 36041292 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1867278
Comparison Time: 00:15:08 (hh:mm:ss) Elapsed Time, 14448 HSPs Collected
Number of families returned by RECON: 3607
Round Time: 00:15:43 (hh:mm:ss) Elapsed Time : 12 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.7Ti7uG/RM_3347510.ThuFeb120649082026
# 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: 00:21:22 (hh:mm:ss) Elapsed Time