RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.sfb6ng/RM_1777423.TueFeb102017092026
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: 1770783428
Database = /data/tmp/rModeler.sfb6ng/GCA_045167005.1_ASM4516700v1 
  - Sequences = 102
  - Bases = 9053467
  - N50 = 292064
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  792376-848939 |                                                   [ 1 ]
  735813-792375 |                                                   [ 1 ]
  679251-735813 |                                                   [ 1 ]
  622688-679250 |                                                   [  ]
  566126-622688 |                                                   [  ]
  509563-566125 |                                                   [ 1 ]
  453001-509563 |                                                   [  ]
  396438-453000 |                                                   [ 1 ]
  339876-396438 |*                                                  [ 2 ]
  283313-339875 |*                                                  [ 2 ]
  226751-283313 |*                                                  [ 2 ]
  170188-226750 |***                                                [ 5 ]
  113626-170188 |*****                                              [ 7 ]
  57063-113625  |**********                                         [ 14 ]
  501-57063     |************************************************** [ 65 ]

Storage Throughput = excellent ( 1672.65 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 9053336 bp ( 9047696 non ambiguous )
   - Num Contigs Represented = 102
   - 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.. : 7 raw families identified
   - RepeatScout: Running filtering stage.. 4 families remaining
   - RepeatScout: 00:00:50 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 4 families... 00:00:06 (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: 00:00:59 (hh:mm:ss) Elapsed Time : 1 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 00:00:21 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       7 repeats masked totaling 2414 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9053336 bp
       Num Contigs Represented = 102
       Non ambiguous bp:
             Initial: 9047696 bp
             After Masking: 8987870 bp
             Masked: 0.66 % 
 -- Input Database Coverage: 9053336 bp out of 9053467 bp ( 100.00 % )
Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 44253
Comparison Time: 00:08:13 (hh:mm:ss) Elapsed Time, 1010 HSPs Collected
Number of families returned by RECON: 341
Round Time: 00:08:39 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 1 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.sfb6ng/RM_1777423.TueFeb102017092026
# 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: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:09:45 (hh:mm:ss) Elapsed Time