RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.zbEx65/RM_380266.MonSep81749382025
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: 1757378977
Database = /data/tmp/rModeler.zbEx65/GCA_002222385.1_Cryp_neof_Ze90_1_V1 
  - Sequences = 164
  - Bases = 18658870
  - N50 = 470770
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  790075-846438 |*                                                  [ 3 ]
  733713-790075 |                                                   [  ]
  677350-733712 |*                                                  [ 3 ]
  620988-677350 |                                                   [ 1 ]
  564626-620988 |                                                   [ 2 ]
  508263-564625 |                                                   [ 1 ]
  451901-508263 |**                                                 [ 6 ]
  395538-451900 |                                                   [ 2 ]
  339176-395538 |*                                                  [ 4 ]
  282814-339176 |                                                   [ 2 ]
  226451-282813 |**                                                 [ 5 ]
  170089-226451 |***                                                [ 8 ]
  113726-170088 |***                                                [ 7 ]
  57364-113726  |******                                             [ 13 ]
  1002-57364    |************************************************** [ 107 ]

Storage Throughput = good ( 806.72 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18658782 bp ( 18219627 non ambiguous )
   - Num Contigs Represented = 164
   - 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.. : 34 raw families identified
   - RepeatScout: Running filtering stage.. 33 families remaining
   - RepeatScout: 00:00:25 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 32 families... 00:00:10 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 7 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:40 (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 : 00:00:01 (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...
       416 repeats masked totaling 88106 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10250834 bp
       Num Contigs Represented = 112
       Non ambiguous bp:
             Initial: 10008092 bp
             After Masking: 9909782 bp
             Masked: 0.98 % 
 -- Input Database Coverage: 10250834 bp out of 18658870 bp ( 54.94 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 50086
Comparison Time: 00:06:31 (hh:mm:ss) Elapsed Time, 2113 HSPs Collected
Number of families returned by RECON: 693
Round Time: 00:07:04 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 38658870


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38658870 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       381 repeats masked totaling 84528 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8407901 bp
       Num Contigs Represented = 105
       Non ambiguous bp:
             Initial: 8211488 bp
             After Masking: 8118724 bp
             Masked: 1.13 % 
 -- Input Database Coverage: 18658735 bp out of 18658870 bp ( 100.00 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 37128
Comparison Time: 00:05:35 (hh:mm:ss) Elapsed Time, 1260 HSPs Collected
Number of families returned by RECON: 476
Round Time: 00:06:00 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 27 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.zbEx65/RM_380266.MonSep81749382025
# 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: 00:00:13 (hh:mm:ss) Elapsed Time


Program Time: 00:13:57 (hh:mm:ss) Elapsed Time