RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.W9rzF8/RM_3951661.TueSep90510232025
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: 1757419822
Database = /dev/shm/rModeler.W9rzF8/GCA_009193685.1_ASM919368v1 
  - Sequences = 474
  - Bases = 35409723
  - N50 = 262500
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  803581-860766 |                                                   [ 3 ]
  746397-803581 |                                                   [ 2 ]
  689213-746397 |                                                   [  ]
  632029-689213 |                                                   [  ]
  574845-632029 |                                                   [ 4 ]
  517661-574845 |                                                   [ 2 ]
  460477-517661 |                                                   [ 1 ]
  403293-460477 |                                                   [ 6 ]
  346109-403293 |*                                                  [ 8 ]
  288925-346109 |*                                                  [ 7 ]
  231741-288925 |*                                                  [ 12 ]
  174557-231741 |**                                                 [ 16 ]
  117373-174557 |****                                               [ 28 ]
  60189-117373  |*******                                            [ 52 ]
  3005-60189    |************************************************** [ 333 ]

Storage Throughput = excellent ( 1389.18 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 35409671 bp ( 35405517 non ambiguous )
   - Num Contigs Represented = 474
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 26 raw families identified
   - RepeatScout: Running filtering stage.. 25 families remaining
   - RepeatScout: 00:00:34 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 25 families... 00:00:05 (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: 00:00:42 (hh:mm:ss) Elapsed Time : 24 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       183 repeats masked totaling 50881 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10038112 bp
       Num Contigs Represented = 193
       Non ambiguous bp:
             Initial: 10037527 bp
             After Masking: 9972095 bp
             Masked: 0.65 % 
 -- Input Database Coverage: 10038112 bp out of 35409723 bp ( 28.35 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 55611
Comparison Time: 00:04:01 (hh:mm:ss) Elapsed Time, 1803 HSPs Collected
Number of families returned by RECON: 793
Round Time: 00:04:12 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 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...
       564 repeats masked totaling 152836 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 25371479 bp
       Num Contigs Represented = 391
       Non ambiguous bp:
             Initial: 25367910 bp
             After Masking: 25173810 bp
             Masked: 0.77 % 
 -- Input Database Coverage: 35409591 bp out of 35409723 bp ( 100.00 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 369370
Comparison Time: 00:13:34 (hh:mm:ss) Elapsed Time, 13183 HSPs Collected
Number of families returned by RECON: 3464
Round Time: 00:14:19 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 34 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.W9rzF8/RM_3951661.TueSep90510232025
# 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: 00:19:21 (hh:mm:ss) Elapsed Time