RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.bBO97G/RM_791409.WedSep101409152025
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: 1757538554
Database = /dev/shm/rModeler.bBO97G/GCA_018154205.1_ASM1815420v1 
  - Sequences = 416
  - Bases = 19543733
  - N50 = 527662
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1742510-1866961 |                                                   [ 1 ]
  1618059-1742509 |                                                   [  ]
  1493608-1618058 |                                                   [  ]
  1369158-1493608 |                                                   [ 1 ]
  1244707-1369157 |                                                   [  ]
  1120256-1244706 |                                                   [  ]
  995805-1120255  |                                                   [ 3 ]
  871355-995805   |                                                   [ 1 ]
  746904-871354   |                                                   [  ]
  622453-746903   |                                                   [  ]
  498002-622452   |                                                   [ 6 ]
  373552-498002   |                                                   [ 6 ]
  249101-373551   |*                                                  [ 9 ]
  124650-249100   |                                                   [ 7 ]
  200-124650      |************************************************** [ 382 ]

Storage Throughput = excellent ( 1665.59 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19543576 bp ( 19538101 non ambiguous )
   - Num Contigs Represented = 416
   - 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.. : 25 raw families identified
   - RepeatScout: Running filtering stage.. 25 families remaining
   - RepeatScout: 00:00:26 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 22 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 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...
       337 repeats masked totaling 63346 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10013754 bp
       Num Contigs Represented = 251
       Non ambiguous bp:
             Initial: 10011275 bp
             After Masking: 9896441 bp
             Masked: 1.15 % 
 -- Input Database Coverage: 10013754 bp out of 19543733 bp ( 51.24 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 102378
Comparison Time: 00:04:50 (hh:mm:ss) Elapsed Time, 18803 HSPs Collected
Number of families returned by RECON: 1649
Round Time: 00:05:23 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 39543733


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39543733 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...
       2099 repeats masked totaling 242517 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9529773 bp
       Num Contigs Represented = 211
       Non ambiguous bp:
             Initial: 9526777 bp
             After Masking: 9227218 bp
             Masked: 3.14 % 
 -- Input Database Coverage: 19543527 bp out of 19543733 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 81406
Comparison Time: 00:04:24 (hh:mm:ss) Elapsed Time, 2909 HSPs Collected
Number of families returned by RECON: 784
Round Time: 00:04:39 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 22 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.bBO97G/RM_791409.WedSep101409152025
# 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: 00:10:42 (hh:mm:ss) Elapsed Time