RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.H0uPMb/RM_1867428.TueFeb102046562026
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: 1770785215
Database = /dev/shm/rModeler.H0uPMb/GCA_045166965.1_ASM4516696v1 
  - Sequences = 127
  - Bases = 9037112
  - N50 = 157658
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  679612-728116 |                                                   [ 1 ]
  631109-679612 |                                                   [  ]
  582605-631108 |                                                   [ 1 ]
  534102-582605 |                                                   [  ]
  485598-534101 |                                                   [ 1 ]
  437095-485598 |                                                   [  ]
  388591-437094 |*                                                  [ 2 ]
  340088-388591 |*                                                  [ 2 ]
  291584-340087 |                                                   [  ]
  243081-291584 |                                                   [  ]
  194577-243080 |*                                                  [ 2 ]
  146074-194577 |***                                                [ 6 ]
  97570-146073  |*******                                            [ 11 ]
  49067-97570   |****************                                   [ 25 ]
  564-49067     |************************************************** [ 76 ]

Storage Throughput = excellent ( 1713.27 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 9037002 bp ( 9029072 non ambiguous )
   - Num Contigs Represented = 127
   - 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.. : 3 raw families identified
   - RepeatScout: Running filtering stage.. 2 families remaining
   - RepeatScout: 00:00:36 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 2 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:00:45 (hh:mm:ss) Elapsed Time : 2 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       20 repeats masked totaling 10301 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9037002 bp
       Num Contigs Represented = 127
       Non ambiguous bp:
             Initial: 9029072 bp
             After Masking: 8956145 bp
             Masked: 0.81 % 
 -- Input Database Coverage: 9037002 bp out of 9037112 bp ( 100.00 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 45451
Comparison Time: 00:07:20 (hh:mm:ss) Elapsed Time, 1078 HSPs Collected
Number of families returned by RECON: 354
Round Time: 00:07:45 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 3 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.H0uPMb/RM_1867428.TueFeb102046562026
# 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: 00:08:36 (hh:mm:ss) Elapsed Time