RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.quZlDG/RM_178541.TueSep92335152025
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: 1757486115
Database = /dev/shm/rModeler.quZlDG/GCA_013145845.1_ASM1314584v1 
  - Sequences = 142
  - Bases = 38941926
  - N50 = 686683
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2134695-2287152 |                                                   [ 1 ]
  1982238-2134694 |                                                   [  ]
  1829782-1982238 |                                                   [  ]
  1677325-1829781 |                                                   [  ]
  1524869-1677325 |                                                   [  ]
  1372412-1524868 |*                                                  [ 2 ]
  1219955-1372411 |*                                                  [ 3 ]
  1067499-1219955 |*                                                  [ 2 ]
  915042-1067498  |                                                   [ 1 ]
  762586-915042   |*                                                  [ 3 ]
  610129-762585   |******                                             [ 11 ]
  457672-610128   |******                                             [ 10 ]
  305216-457672   |********                                           [ 14 ]
  152759-305215   |********                                           [ 14 ]
  303-152759      |************************************************** [ 81 ]

Storage Throughput = excellent ( 1066.93 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38941910 bp ( 38927273 non ambiguous )
   - Num Contigs Represented = 142
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 40 raw families identified
   - RepeatScout: Running filtering stage.. 27 families remaining
   - RepeatScout: 00:01:05 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 24 families... 00:00:25 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:01:42 (hh:mm:ss) Elapsed Time : 21 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 00:00:20 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       265 repeats masked totaling 76754 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10016098 bp
       Num Contigs Represented = 88
       Non ambiguous bp:
             Initial: 10012098 bp
             After Masking: 9921630 bp
             Masked: 0.90 % 
 -- Input Database Coverage: 10016098 bp out of 38941926 bp ( 25.72 % )
Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 37128
Comparison Time: 00:27:34 (hh:mm:ss) Elapsed Time, 2183 HSPs Collected
Number of families returned by RECON: 755
Round Time: 00:41:32 (hh:mm:ss) Elapsed Time : 3 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       791 repeats masked totaling 262375 bp(s).
   - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28925802 bp
       Num Contigs Represented = 127
       Non ambiguous bp:
             Initial: 28915165 bp
             After Masking: 28611930 bp
             Masked: 1.05 % 
 -- Input Database Coverage: 38941900 bp out of 38941926 bp ( 100.00 % )
Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 311655
Comparison Time: 00:59:43 (hh:mm:ss) Elapsed Time, 13267 HSPs Collected
Number of families returned by RECON: 3578
Round Time: 13:09:32 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 33 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.quZlDG/RM_178541.TueSep92335152025
# 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: 00:00:56 (hh:mm:ss) Elapsed Time


Program Time: 13:53:42 (hh:mm:ss) Elapsed Time