RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.b7ugLH/RM_2484845.ThuSep110050362025
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: 1757577035
Database = /dev/shm/rModeler.b7ugLH/GCA_021655875.1_ASM2165587v1 
  - Sequences = 1088
  - Bases = 36824751
  - N50 = 106448
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  355746-381138 |                                                   [ 3 ]
  330355-355746 |                                                   [ 1 ]
  304964-330355 |                                                   [ 2 ]
  279573-304964 |                                                   [ 6 ]
  254182-279573 |                                                   [ 3 ]
  228791-254182 |                                                   [ 8 ]
  203400-228791 |                                                   [ 7 ]
  178009-203400 |                                                   [ 8 ]
  152618-178009 |*                                                  [ 16 ]
  127227-152618 |*                                                  [ 22 ]
  101836-127227 |**                                                 [ 34 ]
  76445-101836  |***                                                [ 54 ]
  51054-76445   |*****                                              [ 74 ]
  25663-51054   |*******                                            [ 112 ]
  272-25663     |************************************************** [ 738 ]

Storage Throughput = excellent ( 1620.97 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36824709 bp ( 36821558 non ambiguous )
   - Num Contigs Represented = 1088
   - 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.. : 31 raw families identified
   - RepeatScout: Running filtering stage.. 28 families remaining
   - RepeatScout: 00:00:39 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 28 families... 00:00:06 (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: 00:00:48 (hh:mm:ss) Elapsed Time : 24 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...
       273 repeats masked totaling 95086 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10011585 bp
       Num Contigs Represented = 392
       Non ambiguous bp:
             Initial: 10010614 bp
             After Masking: 9903243 bp
             Masked: 1.07 % 
 -- Input Database Coverage: 10011585 bp out of 36824751 bp ( 27.19 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 112101
Comparison Time: 00:04:40 (hh:mm:ss) Elapsed Time, 1724 HSPs Collected
Number of families returned by RECON: 607
Round Time: 00:04:55 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       851 repeats masked totaling 229144 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26813106 bp
       Num Contigs Represented = 866
       Non ambiguous bp:
             Initial: 26810926 bp
             After Masking: 26548702 bp
             Masked: 0.98 % 
 -- Input Database Coverage: 36824691 bp out of 36824751 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 795691
Comparison Time: 00:16:08 (hh:mm:ss) Elapsed Time, 10615 HSPs Collected
Number of families returned by RECON: 2955
Round Time: 00:16:42 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 34 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.b7ugLH/RM_2484845.ThuSep110050362025
# 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: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:22:32 (hh:mm:ss) Elapsed Time