RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.kLvcy1/RM_4170747.MonSep81750162025
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: 1757379015
Database = /dev/shm/rModeler.kLvcy1/GCA_002222405.1_Cryp_neof_C8_V1 
  - Sequences = 158
  - Bases = 18629901
  - N50 = 575022
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  830233-889462 |*                                                  [ 3 ]
  771004-830232 |                                                   [ 1 ]
  711775-771003 |                                                   [  ]
  652547-711775 |                                                   [ 2 ]
  593318-652546 |**                                                 [ 5 ]
  534089-593317 |*                                                  [ 3 ]
  474860-534088 |                                                   [ 2 ]
  415632-474860 |                                                   [ 2 ]
  356403-415631 |                                                   [ 2 ]
  297174-356402 |**                                                 [ 6 ]
  237945-297173 |**                                                 [ 6 ]
  178717-237945 |*                                                  [ 3 ]
  119488-178716 |***                                                [ 7 ]
  60259-119487  |**                                                 [ 6 ]
  1031-60259    |*************************************************  [ 110 ]

Storage Throughput = excellent ( 1534.15 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18629786 bp ( 18399430 non ambiguous )
   - Num Contigs Represented = 158
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 30 raw families identified
   - RepeatScout: Running filtering stage.. 30 families remaining
   - RepeatScout: 00:00:17 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 30 families... 00:00:07 (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: 00:00:26 (hh:mm:ss) Elapsed Time : 27 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...
       432 repeats masked totaling 148667 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10175941 bp
       Num Contigs Represented = 97
       Non ambiguous bp:
             Initial: 10036760 bp
             After Masking: 9877271 bp
             Masked: 1.59 % 
 -- Input Database Coverage: 10175941 bp out of 18629901 bp ( 54.62 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 49141
Comparison Time: 00:03:59 (hh:mm:ss) Elapsed Time, 2622 HSPs Collected
Number of families returned by RECON: 699
Round Time: 00:04:14 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 38629901


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38629901 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       524 repeats masked totaling 142206 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8453804 bp
       Num Contigs Represented = 108
       Non ambiguous bp:
             Initial: 8362629 bp
             After Masking: 8213466 bp
             Masked: 1.78 % 
 -- Input Database Coverage: 18629745 bp out of 18629901 bp ( 100.00 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 37401
Comparison Time: 00:03:18 (hh:mm:ss) Elapsed Time, 1195 HSPs Collected
Number of families returned by RECON: 488
Round Time: 00:03:28 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 32 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.kLvcy1/RM_4170747.MonSep81750162025
# 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: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:08:16 (hh:mm:ss) Elapsed Time