RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.Nvf1cb/RM_4162611.FriSep121914002025
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: 1757729639
Database = /dev/shm/rModeler.Nvf1cb/GCA_051397215.1_GA10_18 
  - Sequences = 222
  - Bases = 38540382
  - N50 = 759846
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1551880-1662693 |                                                   [ 1 ]
  1441067-1551879 |                                                   [ 1 ]
  1330254-1441066 |                                                   [  ]
  1219441-1330253 |                                                   [ 2 ]
  1108628-1219440 |                                                   [ 1 ]
  997815-1108627  |*                                                  [ 4 ]
  887002-997814   |                                                   [ 3 ]
  776190-887002   |*                                                  [ 5 ]
  665377-776189   |*                                                  [ 4 ]
  554564-665376   |**                                                 [ 8 ]
  443751-554563   |                                                   [ 2 ]
  332938-443750   |****                                               [ 13 ]
  222125-332937   |**                                                 [ 9 ]
  111312-222124   |****                                               [ 13 ]
  500-111312      |************************************************** [ 156 ]

Storage Throughput = excellent ( 1520.10 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38540359 bp ( 38539878 non ambiguous )
   - Num Contigs Represented = 222
   - 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.. : 24 raw families identified
   - RepeatScout: Running filtering stage.. 21 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 19 families... 00:00:07 (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: 00:00:48 (hh:mm:ss) Elapsed Time : 18 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...
       220 repeats masked totaling 56774 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10007489 bp
       Num Contigs Represented = 111
       Non ambiguous bp:
             Initial: 10007376 bp
             After Masking: 9935385 bp
             Masked: 0.72 % 
 -- Input Database Coverage: 10007489 bp out of 38540382 bp ( 25.97 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 45150
Comparison Time: 00:03:57 (hh:mm:ss) Elapsed Time, 1725 HSPs Collected
Number of families returned by RECON: 777
Round Time: 00:04:11 (hh:mm:ss) Elapsed Time : 2 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       633 repeats masked totaling 157263 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28532812 bp
       Num Contigs Represented = 183
       Non ambiguous bp:
             Initial: 28532444 bp
             After Masking: 28334227 bp
             Masked: 0.69 % 
 -- Input Database Coverage: 38540301 bp out of 38540382 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 340725
Comparison Time: 00:14:59 (hh:mm:ss) Elapsed Time, 13235 HSPs Collected
Number of families returned by RECON: 3518
Round Time: 00:15:38 (hh:mm:ss) Elapsed Time : 5 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.Nvf1cb/RM_4162611.FriSep121914002025
# 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: 00:20:44 (hh:mm:ss) Elapsed Time