RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.W1AEGT/RM_17565.MonSep81339342025
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: 1757363973
Database = /data/tmp/rModeler.W1AEGT/GCA_001466525.1_ASM146652v1 
  - Sequences = 119
  - Bases = 12622465
  - N50 = 397610
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  791224-847663 |                                                   [ 1 ]
  734785-791223 |                                                   [  ]
  678346-734784 |                                                   [ 1 ]
  621907-678345 |                                                   [ 1 ]
  565468-621906 |                                                   [ 1 ]
  509029-565467 |                                                   [ 1 ]
  452590-509028 |*                                                  [ 2 ]
  396152-452590 |**                                                 [ 4 ]
  339713-396151 |*                                                  [ 2 ]
  283274-339712 |**                                                 [ 4 ]
  226835-283273 |**                                                 [ 3 ]
  170396-226834 |                                                   [ 1 ]
  113957-170395 |****                                               [ 6 ]
  57518-113956  |***************                                    [ 22 ]
  1080-57518    |************************************************** [ 70 ]

Storage Throughput = excellent ( 1445.43 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12622345 bp ( 12612987 non ambiguous )
   - Num Contigs Represented = 119
   - 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.. : 22 raw families identified
   - RepeatScout: Running filtering stage.. 20 families remaining
   - RepeatScout: 00:00:22 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 16 families... 00:00:06 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:31 (hh:mm:ss) Elapsed Time : 15 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       228 repeats masked totaling 58982 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10040667 bp
       Num Contigs Represented = 105
       Non ambiguous bp:
             Initial: 10033210 bp
             After Masking: 9909069 bp
             Masked: 1.24 % 
 -- Input Database Coverage: 10040667 bp out of 12622465 bp ( 79.55 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 49455
Comparison Time: 00:04:47 (hh:mm:ss) Elapsed Time, 3188 HSPs Collected
Number of families returned by RECON: 821
Round Time: 00:05:06 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 32622465


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32622465 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       75 repeats masked totaling 21850 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2581647 bp
       Num Contigs Represented = 47
       Non ambiguous bp:
             Initial: 2579746 bp
             After Masking: 2522525 bp
             Masked: 2.22 % 
 -- Input Database Coverage: 12622314 bp out of 12622465 bp ( 100.00 % )
Sampling Time: 00:00:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 3240
Comparison Time: 00:00:57 (hh:mm:ss) Elapsed Time, 174 HSPs Collected
Number of families returned by RECON: 63
Round Time: 00:01:03 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 16 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.W1AEGT/RM_17565.MonSep81339342025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:06:46 (hh:mm:ss) Elapsed Time