RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.LsW1Dk/RM_3106638.MonSep81737262025
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: 1757378245
Database = /data/tmp/rModeler.LsW1Dk/GCA_002222215.1_Cryp_neof_grubii_A5-35-17_V1 
  - Sequences = 592
  - Bases = 18811654
  - N50 = 170666
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  433041-463902 |                                                   [ 3 ]
  402181-433041 |                                                   [  ]
  371321-402181 |                                                   [ 1 ]
  340461-371321 |                                                   [ 1 ]
  309601-340461 |                                                   [ 2 ]
  278741-309601 |                                                   [ 2 ]
  247881-278741 |                                                   [ 3 ]
  217020-247880 |                                                   [ 4 ]
  186160-217020 |*                                                  [ 15 ]
  155300-186160 |*                                                  [ 12 ]
  124440-155300 |*                                                  [ 12 ]
  93580-124440  |*                                                  [ 18 ]
  62720-93580   |**                                                 [ 22 ]
  31860-62720   |****                                               [ 43 ]
  1000-31860    |************************************************** [ 454 ]

Storage Throughput = good ( 997.67 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18811546 bp ( 18811232 non ambiguous )
   - Num Contigs Represented = 592
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 28 raw families identified
   - RepeatScout: Running filtering stage.. 28 families remaining
   - RepeatScout: 00:00:30 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 26 families... 00:00:06 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:00:44 (hh:mm:ss) Elapsed Time : 25 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       353 repeats masked totaling 91829 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10022209 bp
       Num Contigs Represented = 351
       Non ambiguous bp:
             Initial: 10021950 bp
             After Masking: 9920044 bp
             Masked: 1.02 % 
 -- Input Database Coverage: 10022209 bp out of 18811654 bp ( 53.28 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 124251
Comparison Time: 00:07:17 (hh:mm:ss) Elapsed Time, 2527 HSPs Collected
Number of families returned by RECON: 778
Round Time: 00:07:59 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 38811654


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38811654 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       373 repeats masked totaling 102459 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8789257 bp
       Num Contigs Represented = 331
       Non ambiguous bp:
             Initial: 8789202 bp
             After Masking: 8677609 bp
             Masked: 1.27 % 
 -- Input Database Coverage: 18811466 bp out of 18811654 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 105570
Comparison Time: 00:06:35 (hh:mm:ss) Elapsed Time, 1644 HSPs Collected
Number of families returned by RECON: 605
Round Time: 00:07:21 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.LsW1Dk/RM_3106638.MonSep81737262025
# 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: 00:00:18 (hh:mm:ss) Elapsed Time


Program Time: 00:16:22 (hh:mm:ss) Elapsed Time