RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.gLljRd/RM_4056907.TueSep90444432025
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: 1757418282
Database = /dev/shm/rModeler.gLljRd/GCA_004802665.1_ASM480266v1 
  - Sequences = 1328
  - Bases = 36879476
  - N50 = 62751
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  359354-384982 |                                                   [ 1 ]
  333726-359353 |                                                   [ 1 ]
  308099-333726 |                                                   [  ]
  282471-308098 |                                                   [  ]
  256843-282470 |                                                   [ 3 ]
  231216-256843 |                                                   [ 1 ]
  205588-231215 |                                                   [ 4 ]
  179960-205587 |                                                   [ 2 ]
  154333-179960 |                                                   [ 7 ]
  128705-154332 |*                                                  [ 22 ]
  103077-128704 |*                                                  [ 31 ]
  77450-103077  |**                                                 [ 50 ]
  51822-77449   |*****                                              [ 92 ]
  26194-51821   |***********                                        [ 211 ]
  567-26194     |************************************************** [ 903 ]

Storage Throughput = excellent ( 1607.18 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36879446 bp ( 36841369 non ambiguous )
   - Num Contigs Represented = 1328
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 228 raw families identified
   - RepeatScout: Running filtering stage.. 223 families remaining
   - RepeatScout: 00:00:46 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 223 families... 00:00:32 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 49 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:23 (hh:mm:ss) Elapsed Time : 174 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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2048 repeats masked totaling 742781 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10022054 bp
       Num Contigs Represented = 468
       Non ambiguous bp:
             Initial: 10010087 bp
             After Masking: 9261314 bp
             Masked: 7.48 % 
 -- Input Database Coverage: 10022054 bp out of 36879476 bp ( 27.18 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 133386
Comparison Time: 00:04:42 (hh:mm:ss) Elapsed Time, 4896 HSPs Collected
Number of families returned by RECON: 1104
Round Time: 00:04:57 (hh:mm:ss) Elapsed Time : 4 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5840 repeats masked totaling 2044292 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26857391 bp
       Num Contigs Represented = 1001
       Non ambiguous bp:
             Initial: 26831281 bp
             After Masking: 24759098 bp
             Masked: 7.72 % 
 -- Input Database Coverage: 36879445 bp out of 36879476 bp ( 100.00 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 850860
Comparison Time: 00:15:35 (hh:mm:ss) Elapsed Time, 25928 HSPs Collected
Number of families returned by RECON: 3730
Round Time: 00:16:36 (hh:mm:ss) Elapsed Time : 20 families discovered.

RepeatScout/RECON discovery complete: 198 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.gLljRd/RM_4056907.TueSep90444432025
# 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: 00:00:23 (hh:mm:ss) Elapsed Time


Program Time: 00:23:19 (hh:mm:ss) Elapsed Time