RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.mc3c6d/RM_4039313.MonSep81233152025
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: 1757359994
Database = /dev/shm/rModeler.mc3c6d/GCA_000786445.1_R265.1 
  - Sequences = 779
  - Bases = 17256624
  - N50 = 72449
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  225928-242052 |                                                   [ 3 ]
  209805-225928 |                                                   [ 2 ]
  193681-209804 |                                                   [ 2 ]
  177558-193681 |                                                   [ 1 ]
  161434-177557 |                                                   [ 2 ]
  145311-161434 |                                                   [ 5 ]
  129187-145310 |                                                   [ 4 ]
  113064-129187 |                                                   [ 8 ]
  96940-113063  |**                                                 [ 23 ]
  80817-96940   |*                                                  [ 12 ]
  64693-80816   |*                                                  [ 18 ]
  48570-64693   |****                                               [ 42 ]
  32446-48569   |*****                                              [ 60 ]
  16323-32446   |*******                                            [ 76 ]
  200-16323     |************************************************** [ 521 ]

Storage Throughput = excellent ( 1656.92 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 17256551 bp ( 17255781 non ambiguous )
   - Num Contigs Represented = 779
   - 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.. : 9 raw families identified
   - RepeatScout: Running filtering stage.. 8 families remaining
   - RepeatScout: 00:00:14 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 7 families... 00:00:04 (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: 00:00:21 (hh:mm:ss) Elapsed Time : 6 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       201 repeats masked totaling 41843 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10006309 bp
       Num Contigs Represented = 496
       Non ambiguous bp:
             Initial: 10005901 bp
             After Masking: 9954665 bp
             Masked: 0.51 % 
 -- Input Database Coverage: 10006309 bp out of 17256624 bp ( 57.99 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 178503
Comparison Time: 00:04:53 (hh:mm:ss) Elapsed Time, 2197 HSPs Collected
Number of families returned by RECON: 686
Round Time: 00:05:07 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 37256624


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 37256624 bp
   - Sequence extraction : 00:00:00 (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...
       150 repeats masked totaling 34167 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 7250223 bp
       Num Contigs Represented = 378
       Non ambiguous bp:
             Initial: 7249861 bp
             After Masking: 7210319 bp
             Masked: 0.55 % 
 -- Input Database Coverage: 17256532 bp out of 17256624 bp ( 100.00 % )
Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 98790
Comparison Time: 00:03:33 (hh:mm:ss) Elapsed Time, 891 HSPs Collected
Number of families returned by RECON: 360
Round Time: 00:03:39 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 8 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.mc3c6d/RM_4039313.MonSep81233152025
# 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: 00:09:13 (hh:mm:ss) Elapsed Time