RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.PVIGbf/RM_1521680.FriSep122026272025
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: 1757733986
Database = /dev/shm/rModeler.PVIGbf/GCA_051397635.1_GA10_15 
  - Sequences = 202
  - Bases = 38566800
  - N50 = 937344
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2153812-2307621 |                                                   [ 2 ]
  2000004-2153812 |                                                   [  ]
  1846196-2000004 |                                                   [ 2 ]
  1692388-1846196 |                                                   [ 1 ]
  1538580-1692388 |                                                   [  ]
  1384772-1538580 |                                                   [ 1 ]
  1230964-1384772 |                                                   [ 1 ]
  1077156-1230964 |                                                   [ 3 ]
  923348-1077156  |                                                   [ 3 ]
  769540-923348   |                                                   [ 3 ]
  615732-769540   |*                                                  [ 6 ]
  461924-615732   |**                                                 [ 8 ]
  308116-461924   |**                                                 [ 9 ]
  154308-308116   |***                                                [ 11 ]
  500-154308      |************************************************** [ 152 ]

Storage Throughput = excellent ( 1648.33 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38566731 bp ( 38566534 non ambiguous )
   - Num Contigs Represented = 202
   - 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.. : 25 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:00:39 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 19 families... 00:00:08 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:51 (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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       193 repeats masked totaling 49514 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10025328 bp
       Num Contigs Represented = 82
       Non ambiguous bp:
             Initial: 10025324 bp
             After Masking: 9960032 bp
             Masked: 0.65 % 
 -- Input Database Coverage: 10025328 bp out of 38566800 bp ( 25.99 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 40186
Comparison Time: 00:03:41 (hh:mm:ss) Elapsed Time, 1715 HSPs Collected
Number of families returned by RECON: 791
Round Time: 00:03:59 (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...
       643 repeats masked totaling 170176 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28541323 bp
       Num Contigs Represented = 178
       Non ambiguous bp:
             Initial: 28541130 bp
             After Masking: 28328912 bp
             Masked: 0.74 % 
 -- Input Database Coverage: 38566651 bp out of 38566800 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 347361
Comparison Time: 00:15:03 (hh:mm:ss) Elapsed Time, 14356 HSPs Collected
Number of families returned by RECON: 3570
Round Time: 00:15:43 (hh:mm:ss) Elapsed Time : 14 families discovered.

RepeatScout/RECON discovery complete: 34 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.PVIGbf/RM_1521680.FriSep122026272025
# 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: 00:20:41 (hh:mm:ss) Elapsed Time