RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.Ff0jiZ/RM_2283684.ThuSep110036592025
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: 1757576219
Database = /dev/shm/rModeler.Ff0jiZ/GCA_021018955.2_ASM2101895v2 
  - Sequences = 2230
  - Bases = 14506990
  - N50 = 23076
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  133721-143259 |                                                   [ 1 ]
  124184-133721 |                                                   [ 1 ]
  114647-124184 |                                                   [  ]
  105109-114646 |                                                   [ 1 ]
  95572-105109  |                                                   [ 3 ]
  86035-95572   |                                                   [ 3 ]
  76498-86035   |                                                   [ 2 ]
  66960-76497   |                                                   [ 8 ]
  57423-66960   |                                                   [ 7 ]
  47886-57423   |                                                   [ 11 ]
  38349-47886   |                                                   [ 27 ]
  28811-38348   |*                                                  [ 66 ]
  19274-28811   |**                                                 [ 104 ]
  9737-19274    |******                                             [ 214 ]
  200-9737      |************************************************** [ 1782 ]

Storage Throughput = excellent ( 1665.84 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14506945 bp ( 14192162 non ambiguous )
   - Num Contigs Represented = 2230
   - 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.. : 36 raw families identified
   - RepeatScout: Running filtering stage.. 33 families remaining
   - RepeatScout: 00:00:58 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 30 families... 00:00:06 (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: 00:01:07 (hh:mm:ss) Elapsed Time : 27 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       569 repeats masked totaling 156343 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10225583 bp
       Num Contigs Represented = 1594
       Non ambiguous bp:
             Initial: 10003979 bp
             After Masking: 9811624 bp
             Masked: 1.92 % 
 -- Input Database Coverage: 10225583 bp out of 14506990 bp ( 70.49 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1324378
Comparison Time: 00:09:55 (hh:mm:ss) Elapsed Time, 6007 HSPs Collected
Number of families returned by RECON: 1376
Round Time: 00:10:26 (hh:mm:ss) Elapsed Time : 5 families discovered.
   - Increasing sample size to include end piece now = 34506990


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34506990 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...
       308 repeats masked totaling 74042 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4281305 bp
       Num Contigs Represented = 665
       Non ambiguous bp:
             Initial: 4188126 bp
             After Masking: 4099608 bp
             Masked: 2.11 % 
 -- Input Database Coverage: 14506888 bp out of 14506990 bp ( 100.00 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 225456
Comparison Time: 00:03:34 (hh:mm:ss) Elapsed Time, 727 HSPs Collected
Number of families returned by RECON: 335
Round Time: 00:03:41 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 32 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.Ff0jiZ/RM_2283684.ThuSep110036592025
# 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: 00:15:20 (hh:mm:ss) Elapsed Time