RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.rIJrYJ/RM_3821631.FriSep122101582025
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: 1757736117
Database = /dev/shm/rModeler.rIJrYJ/GCA_051397735.1_GA10_17 
  - Sequences = 207
  - Bases = 38581706
  - N50 = 1196607
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2468743-2645046 |                                                   [ 1 ]
  2292440-2468742 |                                                   [  ]
  2116138-2292440 |                                                   [ 1 ]
  1939835-2116137 |                                                   [ 1 ]
  1763532-1939834 |                                                   [  ]
  1587230-1763532 |                                                   [ 1 ]
  1410927-1587229 |                                                   [ 2 ]
  1234624-1410926 |*                                                  [ 4 ]
  1058322-1234624 |                                                   [ 2 ]
  882019-1058321  |*                                                  [ 4 ]
  705716-882018   |                                                   [ 2 ]
  529414-705716   |*                                                  [ 6 ]
  353111-529413   |**                                                 [ 9 ]
  176808-353110   |****                                               [ 13 ]
  506-176808      |************************************************** [ 161 ]

Storage Throughput = excellent ( 1777.87 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38581566 bp ( 38581041 non ambiguous )
   - Num Contigs Represented = 207
   - 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.. : 29 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:00:36 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 20 families... 00:00:09 (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: 00:00:50 (hh:mm:ss) Elapsed Time : 19 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       196 repeats masked totaling 29799 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10032862 bp
       Num Contigs Represented = 102
       Non ambiguous bp:
             Initial: 10032785 bp
             After Masking: 9989178 bp
             Masked: 0.43 % 
 -- Input Database Coverage: 10032862 bp out of 38581706 bp ( 26.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 43660
Comparison Time: 00:03:52 (hh:mm:ss) Elapsed Time, 1931 HSPs Collected
Number of families returned by RECON: 793
Round Time: 00:04:10 (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 : 00:00:02 (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...
       647 repeats masked totaling 188026 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28548629 bp
       Num Contigs Represented = 166
       Non ambiguous bp:
             Initial: 28548181 bp
             After Masking: 28316366 bp
             Masked: 0.81 % 
 -- Input Database Coverage: 38581491 bp out of 38581706 bp ( 100.00 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 343206
Comparison Time: 00:15:01 (hh:mm:ss) Elapsed Time, 14011 HSPs Collected
Number of families returned by RECON: 3578
Round Time: 00:15:45 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 30 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.rIJrYJ/RM_3821631.FriSep122101582025
# 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: 00:20:53 (hh:mm:ss) Elapsed Time