RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.SAFG4S/RM_2132058.MonSep81750332025
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: 1757379032
Database = /dev/shm/rModeler.SAFG4S/GCA_002222395.1_Cryp_neof_MW_RSA36_V1 
  - Sequences = 457
  - Bases = 18447467
  - N50 = 186239
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  576201-617286 |                                                   [ 1 ]
  535116-576200 |                                                   [ 1 ]
  494031-535115 |                                                   [ 1 ]
  452946-494030 |                                                   [  ]
  411862-452946 |                                                   [ 1 ]
  370777-411861 |                                                   [ 1 ]
  329692-370776 |                                                   [ 3 ]
  288607-329691 |                                                   [ 2 ]
  247522-288606 |*                                                  [ 9 ]
  206438-247522 |                                                   [ 6 ]
  165353-206437 |*                                                  [ 13 ]
  124268-165352 |*                                                  [ 13 ]
  83183-124267  |**                                                 [ 19 ]
  42098-83182   |*****                                              [ 37 ]
  1014-42098    |************************************************** [ 350 ]

Storage Throughput = excellent ( 1630.29 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18447379 bp ( 18447278 non ambiguous )
   - Num Contigs Represented = 457
   - 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.. : 41 raw families identified
   - RepeatScout: Running filtering stage.. 41 families remaining
   - RepeatScout: 00:00:18 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 40 families... 00:00:07 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:28 (hh:mm:ss) Elapsed Time : 36 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:01 (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...
       560 repeats masked totaling 263647 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10008663 bp
       Num Contigs Represented = 278
       Non ambiguous bp:
             Initial: 10008562 bp
             After Masking: 9734744 bp
             Masked: 2.74 % 
 -- Input Database Coverage: 10008663 bp out of 18447467 bp ( 54.25 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 93528
Comparison Time: 00:04:27 (hh:mm:ss) Elapsed Time, 3216 HSPs Collected
Number of families returned by RECON: 728
Round Time: 00:04:43 (hh:mm:ss) Elapsed Time : 5 families discovered.
   - Increasing sample size to include end piece now = 38447467


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38447467 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...
       574 repeats masked totaling 259375 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8438671 bp
       Num Contigs Represented = 264
       Non ambiguous bp:
             Initial: 8438671 bp
             After Masking: 8170688 bp
             Masked: 3.18 % 
 -- Input Database Coverage: 18447334 bp out of 18447467 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 73536
Comparison Time: 00:03:42 (hh:mm:ss) Elapsed Time, 1214 HSPs Collected
Number of families returned by RECON: 509
Round Time: 00:03:51 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 41 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.SAFG4S/RM_2132058.MonSep81750332025
# 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: 00:00:10 (hh:mm:ss) Elapsed Time


Program Time: 00:09:12 (hh:mm:ss) Elapsed Time