RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.uo0MMp/RM_2931543.WedSep101401502025
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: 1757538109
Database = /dev/shm/rModeler.uo0MMp/GCA_018154035.1_ASM1815403v1 
  - Sequences = 496
  - Bases = 19547534
  - N50 = 352516
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1055129-1130482 |                                                   [ 1 ]
  979777-1055129  |                                                   [ 1 ]
  904425-979777   |                                                   [  ]
  829073-904425   |                                                   [ 3 ]
  753721-829073   |                                                   [  ]
  678369-753721   |                                                   [  ]
  603017-678369   |                                                   [ 1 ]
  527664-603016   |                                                   [  ]
  452312-527664   |                                                   [ 4 ]
  376960-452312   |                                                   [ 2 ]
  301608-376960   |*                                                  [ 9 ]
  226256-301608   |                                                   [ 8 ]
  150904-226256   |*                                                  [ 14 ]
  75552-150904    |*                                                  [ 17 ]
  200-75552       |*************************************************  [ 436 ]

Storage Throughput = excellent ( 1483.69 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19547377 bp ( 19539467 non ambiguous )
   - Num Contigs Represented = 496
   - Sequence extraction : 00:00:00 (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.. 23 families remaining
   - RepeatScout: 00:00:28 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 21 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:34 (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 : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       317 repeats masked totaling 49523 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10005718 bp
       Num Contigs Represented = 284
       Non ambiguous bp:
             Initial: 10001626 bp
             After Masking: 9895670 bp
             Masked: 1.06 % 
 -- Input Database Coverage: 10005718 bp out of 19547534 bp ( 51.19 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 112101
Comparison Time: 00:04:57 (hh:mm:ss) Elapsed Time, 18460 HSPs Collected
Number of families returned by RECON: 1583
Round Time: 00:05:28 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 39547534


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39547534 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2333 repeats masked totaling 219187 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9541579 bp
       Num Contigs Represented = 280
       Non ambiguous bp:
             Initial: 9537761 bp
             After Masking: 9262506 bp
             Masked: 2.89 % 
 -- Input Database Coverage: 19547297 bp out of 19547534 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 104196
Comparison Time: 00:04:33 (hh:mm:ss) Elapsed Time, 3544 HSPs Collected
Number of families returned by RECON: 808
Round Time: 00:04:48 (hh:mm:ss) Elapsed Time : 3 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.uo0MMp/RM_2931543.WedSep101401502025
# 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: 00:00:05 (hh:mm:ss) Elapsed Time


Program Time: 00:10:55 (hh:mm:ss) Elapsed Time