RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.qfyXVx/RM_1554783.FriSep122029122025
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: 1757734152
Database = /dev/shm/rModeler.qfyXVx/GCA_051397645.1_GA1_2 
  - Sequences = 273
  - Bases = 38570705
  - N50 = 567624
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1778684-1905697 |                                                   [ 1 ]
  1651672-1778684 |                                                   [  ]
  1524659-1651671 |                                                   [  ]
  1397647-1524659 |                                                   [ 1 ]
  1270635-1397647 |                                                   [  ]
  1143622-1270634 |                                                   [  ]
  1016610-1143622 |*                                                  [ 4 ]
  889597-1016609  |                                                   [ 1 ]
  762585-889597   |*                                                  [ 5 ]
  635573-762585   |*                                                  [ 5 ]
  508560-635572   |**                                                 [ 9 ]
  381548-508560   |*                                                  [ 7 ]
  254535-381547   |*****                                              [ 21 ]
  127523-254535   |******                                             [ 24 ]
  511-127523      |************************************************** [ 195 ]

Storage Throughput = excellent ( 1765.71 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38570664 bp ( 38570167 non ambiguous )
   - Num Contigs Represented = 273
   - 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.. : 32 raw families identified
   - RepeatScout: Running filtering stage.. 28 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 26 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:47 (hh:mm:ss) Elapsed Time : 24 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       224 repeats masked totaling 66571 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10000712 bp
       Num Contigs Represented = 126
       Non ambiguous bp:
             Initial: 10000595 bp
             After Masking: 9919485 bp
             Masked: 0.81 % 
 -- Input Database Coverage: 10000712 bp out of 38570705 bp ( 25.93 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 45451
Comparison Time: 00:03:49 (hh:mm:ss) Elapsed Time, 1785 HSPs Collected
Number of families returned by RECON: 719
Round Time: 00:04:03 (hh:mm:ss) Elapsed Time : 1 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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       631 repeats masked totaling 135300 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28569902 bp
       Num Contigs Represented = 228
       Non ambiguous bp:
             Initial: 28569522 bp
             After Masking: 28391127 bp
             Masked: 0.62 % 
 -- Input Database Coverage: 38570614 bp out of 38570705 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 371953
Comparison Time: 00:15:02 (hh:mm:ss) Elapsed Time, 14535 HSPs Collected
Number of families returned by RECON: 3670
Round Time: 00:15:38 (hh:mm:ss) Elapsed Time : 5 families discovered.

RepeatScout/RECON discovery complete: 30 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.qfyXVx/RM_1554783.FriSep122029122025
# 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: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:20:35 (hh:mm:ss) Elapsed Time