RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.amnZEI/RM_434435.FriSep121907392025
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: 1757729258
Database = /dev/shm/rModeler.amnZEI/GCA_051397175.1_GA10_2 
  - Sequences = 199
  - Bases = 38433387
  - N50 = 600881
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2056444-2203298 |                                                   [ 1 ]
  1909591-2056444 |                                                   [  ]
  1762738-1909591 |                                                   [  ]
  1615885-1762738 |                                                   [ 1 ]
  1469032-1615885 |                                                   [  ]
  1322179-1469032 |                                                   [  ]
  1175326-1322179 |                                                   [ 1 ]
  1028473-1175326 |                                                   [ 1 ]
  881620-1028473  |*                                                  [ 4 ]
  734767-881620   |*                                                  [ 3 ]
  587914-734767   |***                                                [ 10 ]
  441061-587914   |*****                                              [ 13 ]
  294208-441061   |*****                                              [ 13 ]
  147355-294208   |********                                           [ 23 ]
  502-147355      |************************************************** [ 129 ]

Storage Throughput = excellent ( 1641.72 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38433310 bp ( 38432928 non ambiguous )
   - Num Contigs Represented = 199
   - 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.. : 24 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 20 families... 00:00:05 (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: 00:00:47 (hh:mm:ss) Elapsed Time : 20 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...
       210 repeats masked totaling 43138 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10000177 bp
       Num Contigs Represented = 111
       Non ambiguous bp:
             Initial: 10000107 bp
             After Masking: 9946783 bp
             Masked: 0.53 % 
 -- Input Database Coverage: 10000177 bp out of 38433387 bp ( 26.02 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 40186
Comparison Time: 00:03:44 (hh:mm:ss) Elapsed Time, 1811 HSPs Collected
Number of families returned by RECON: 754
Round Time: 00:03:56 (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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       504 repeats masked totaling 98544 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28433053 bp
       Num Contigs Represented = 174
       Non ambiguous bp:
             Initial: 28432741 bp
             After Masking: 28291108 bp
             Masked: 0.50 % 
 -- Input Database Coverage: 38433230 bp out of 38433387 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 333336
Comparison Time: 00:14:45 (hh:mm:ss) Elapsed Time, 13644 HSPs Collected
Number of families returned by RECON: 3641
Round Time: 00:15:21 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 31 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.amnZEI/RM_434435.FriSep121907392025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:20:10 (hh:mm:ss) Elapsed Time