RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.WOppeQ/RM_3823584.TueSep90421012025
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: 1757416861
Database = /dev/shm/rModeler.WOppeQ/GCA_004332465.1_ASM433246v1 
  - Sequences = 207
  - Bases = 12251356
  - N50 = 274427
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1068464-1144748 |                                                   [ 1 ]
  992181-1068464  |                                                   [  ]
  915898-992181   |                                                   [  ]
  839615-915898   |                                                   [ 1 ]
  763332-839615   |                                                   [  ]
  687049-763332   |                                                   [ 1 ]
  610766-687049   |                                                   [ 1 ]
  534482-610765   |                                                   [  ]
  458199-534482   |                                                   [ 2 ]
  381916-458199   |                                                   [ 1 ]
  305633-381916   |                                                   [ 2 ]
  229350-305633   |***                                                [ 10 ]
  153067-229350   |**                                                 [ 9 ]
  76784-153067    |****                                               [ 16 ]
  501-76784       |************************************************** [ 163 ]

Storage Throughput = excellent ( 1168.95 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12251255 bp ( 12247395 non ambiguous )
   - Num Contigs Represented = 207
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 16 raw families identified
   - RepeatScout: Running filtering stage.. 16 families remaining
   - RepeatScout: 00:00:19 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 14 families... 00:00:07 (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: 00:00:29 (hh:mm:ss) Elapsed Time : 14 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 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       223 repeats masked totaling 44272 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10026157 bp
       Num Contigs Represented = 179
       Non ambiguous bp:
             Initial: 10022783 bp
             After Masking: 9930499 bp
             Masked: 0.92 % 
 -- Input Database Coverage: 10026157 bp out of 12251356 bp ( 81.84 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 75078
Comparison Time: 00:04:47 (hh:mm:ss) Elapsed Time, 2818 HSPs Collected
Number of families returned by RECON: 853
Round Time: 00:05:03 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 32251356


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32251356 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       70 repeats masked totaling 16286 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2225018 bp
       Num Contigs Represented = 54
       Non ambiguous bp:
             Initial: 2224532 bp
             After Masking: 2198921 bp
             Masked: 1.15 % 
 -- Input Database Coverage: 12251175 bp out of 12251356 bp ( 100.00 % )
Sampling Time: 00:00:03 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 3570
Comparison Time: 00:00:51 (hh:mm:ss) Elapsed Time, 148 HSPs Collected
Number of families returned by RECON: 87
Round Time: 00:00:54 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 15 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.WOppeQ/RM_3823584.TueSep90421012025
# 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: 00:06:32 (hh:mm:ss) Elapsed Time