RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.cpyFlx/RM_1001305.ThuSep110021532025
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: 1757575313
Database = /dev/shm/rModeler.cpyFlx/GCA_021019025.2_ASM2101902v2 
  - Sequences = 1551
  - Bases = 14351529
  - N50 = 30432
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  350070-375061 |                                                   [ 1 ]
  325079-350069 |                                                   [  ]
  300088-325078 |                                                   [  ]
  275098-300088 |                                                   [  ]
  250107-275097 |                                                   [  ]
  225116-250106 |                                                   [  ]
  200125-225115 |                                                   [  ]
  175135-200125 |                                                   [ 2 ]
  150144-175134 |                                                   [ 2 ]
  125153-150143 |                                                   [ 2 ]
  100162-125152 |                                                   [ 5 ]
  75172-100162  |                                                   [ 12 ]
  50181-75171   |                                                   [ 26 ]
  25190-50180   |****                                               [ 112 ]
  200-25190     |************************************************** [ 1389 ]

Storage Throughput = excellent ( 1609.27 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14351441 bp ( 14132898 non ambiguous )
   - Num Contigs Represented = 1551
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 28 raw families identified
   - RepeatScout: Running filtering stage.. 27 families remaining
   - RepeatScout: 00:00:59 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 26 families... 00:00:13 (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: 00:01:15 (hh:mm:ss) Elapsed Time : 23 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 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       372 repeats masked totaling 136837 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10168379 bp
       Num Contigs Represented = 1104
       Non ambiguous bp:
             Initial: 10014080 bp
             After Masking: 9834936 bp
             Masked: 1.79 % 
 -- Input Database Coverage: 10168379 bp out of 14351529 bp ( 70.85 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 683865
Comparison Time: 00:08:30 (hh:mm:ss) Elapsed Time, 4874 HSPs Collected
Number of families returned by RECON: 1102
Round Time: 00:08:59 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 34351529


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34351529 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...
       206 repeats masked totaling 57183 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4183050 bp
       Num Contigs Represented = 482
       Non ambiguous bp:
             Initial: 4118806 bp
             After Masking: 4045227 bp
             Masked: 1.79 % 
 -- Input Database Coverage: 14351429 bp out of 14351529 bp ( 100.00 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 122760
Comparison Time: 00:02:58 (hh:mm:ss) Elapsed Time, 793 HSPs Collected
Number of families returned by RECON: 320
Round Time: 00:03:12 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.cpyFlx/RM_1001305.ThuSep110021532025
# 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: 00:13:34 (hh:mm:ss) Elapsed Time