RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.Fk8IiK/RM_3918833.TueSep90422312025
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: 1757416950
Database = /dev/shm/rModeler.Fk8IiK/GCA_004332455.1_ASM433245v1 
  - Sequences = 202
  - Bases = 12236919
  - N50 = 426980
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  797011-853905 |                                                   [ 1 ]
  740117-797010 |                                                   [ 1 ]
  683224-740117 |                                                   [ 2 ]
  626330-683223 |                                                   [  ]
  569436-626329 |                                                   [ 1 ]
  512543-569436 |                                                   [ 2 ]
  455649-512542 |                                                   [ 1 ]
  398755-455648 |                                                   [ 3 ]
  341862-398755 |                                                   [ 3 ]
  284968-341861 |                                                   [ 3 ]
  228074-284967 |                                                   [ 2 ]
  171181-228074 |                                                   [ 1 ]
  114287-171180 |***                                                [ 10 ]
  57393-114286  |***                                                [ 12 ]
  500-57393     |************************************************** [ 160 ]

Storage Throughput = excellent ( 1250.23 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12236849 bp ( 12232787 non ambiguous )
   - Num Contigs Represented = 202
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 19 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:18 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 17 families... 00:00:06 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:26 (hh:mm:ss) Elapsed Time : 15 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 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       267 repeats masked totaling 54865 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10042097 bp
       Num Contigs Represented = 175
       Non ambiguous bp:
             Initial: 10038613 bp
             After Masking: 9939327 bp
             Masked: 0.99 % 
 -- Input Database Coverage: 10042097 bp out of 12236919 bp ( 82.06 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 76245
Comparison Time: 00:04:41 (hh:mm:ss) Elapsed Time, 2652 HSPs Collected
Number of families returned by RECON: 806
Round Time: 00:04:52 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 32236919


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32236919 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...
       63 repeats masked totaling 13179 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2194680 bp
       Num Contigs Represented = 53
       Non ambiguous bp:
             Initial: 2194102 bp
             After Masking: 2171280 bp
             Masked: 1.04 % 
 -- Input Database Coverage: 12236777 bp out of 12236919 bp ( 100.00 % )
Sampling Time: 00:00:03 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 3240
Comparison Time: 00:00:49 (hh:mm:ss) Elapsed Time, 112 HSPs Collected
Number of families returned by RECON: 74
Round Time: 00:00:52 (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.Fk8IiK/RM_3918833.TueSep90422312025
# 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: 00:06:16 (hh:mm:ss) Elapsed Time