RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.tFo6Fm/RM_2898748.MonSep81739122025
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: 1757378351
Database = /dev/shm/rModeler.tFo6Fm/GCA_002222255.1_Cryp_neof_D17_1_V1 
  - Sequences = 537
  - Bases = 18639132
  - N50 = 175623
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  593375-635688 |                                                   [ 1 ]
  551063-593375 |                                                   [  ]
  508751-551063 |                                                   [  ]
  466439-508751 |                                                   [ 1 ]
  424127-466439 |                                                   [ 1 ]
  381814-424126 |                                                   [ 4 ]
  339502-381814 |                                                   [ 1 ]
  297190-339502 |                                                   [ 2 ]
  254878-297190 |                                                   [ 7 ]
  212566-254878 |                                                   [ 7 ]
  170253-212565 |                                                   [ 8 ]
  127941-170253 |*                                                  [ 12 ]
  85629-127941  |***                                                [ 31 ]
  43317-85629   |****                                               [ 37 ]
  1005-43317    |************************************************** [ 425 ]

Storage Throughput = excellent ( 1677.53 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18639004 bp ( 18638904 non ambiguous )
   - Num Contigs Represented = 537
   - 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.. : 45 raw families identified
   - RepeatScout: Running filtering stage.. 45 families remaining
   - RepeatScout: 00:00:20 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 44 families... 00:00:11 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 6 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 : 38 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...
       639 repeats masked totaling 431154 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10031548 bp
       Num Contigs Represented = 341
       Non ambiguous bp:
             Initial: 10031548 bp
             After Masking: 9590536 bp
             Masked: 4.40 % 
 -- Input Database Coverage: 10031548 bp out of 18639132 bp ( 53.82 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 122265
Comparison Time: 00:04:42 (hh:mm:ss) Elapsed Time, 3034 HSPs Collected
Number of families returned by RECON: 659
Round Time: 00:04:57 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 38639132


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38639132 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...
       554 repeats masked totaling 313936 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8607393 bp
       Num Contigs Represented = 277
       Non ambiguous bp:
             Initial: 8607293 bp
             After Masking: 8285694 bp
             Masked: 3.74 % 
 -- Input Database Coverage: 18638941 bp out of 18639132 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 79401
Comparison Time: 00:03:51 (hh:mm:ss) Elapsed Time, 1330 HSPs Collected
Number of families returned by RECON: 515
Round Time: 00:04:04 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 42 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.tFo6Fm/RM_2898748.MonSep81739122025
# 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: 00:00:12 (hh:mm:ss) Elapsed Time


Program Time: 00:09:47 (hh:mm:ss) Elapsed Time