RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.gt9ZX3/RM_539628.ThuSep110927262025
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: 1757608046
Database = /dev/shm/rModeler.gt9ZX3/GCA_024322255.1_AFRL_Nalb_1.0 
  - Sequences = 234
  - Bases = 20667795
  - N50 = 533615
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1043757-1118297 |                                                   [ 2 ]
  969217-1043756  |                                                   [ 1 ]
  894678-969217   |                                                   [ 1 ]
  820138-894677   |                                                   [ 1 ]
  745598-820137   |                                                   [ 2 ]
  671059-745598   |                                                   [ 1 ]
  596519-671058   |                                                   [ 2 ]
  521979-596518   |                                                   [ 3 ]
  447440-521979   |                                                   [ 3 ]
  372900-447439   |*                                                  [ 6 ]
  298360-372899   |                                                   [ 1 ]
  223821-298360   |*                                                  [ 4 ]
  149281-223820   |**                                                 [ 8 ]
  74741-149280    |*****                                              [ 21 ]
  202-74741       |************************************************** [ 178 ]

Storage Throughput = excellent ( 1672.05 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 20667741 bp ( 20666246 non ambiguous )
   - Num Contigs Represented = 234
   - 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.. : 27 raw families identified
   - RepeatScout: Running filtering stage.. 27 families remaining
   - RepeatScout: 00:00:18 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 27 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 7 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 : 20 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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       455 repeats masked totaling 105444 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10032519 bp
       Num Contigs Represented = 141
       Non ambiguous bp:
             Initial: 10031909 bp
             After Masking: 9914395 bp
             Masked: 1.17 % 
 -- Input Database Coverage: 10032519 bp out of 20667795 bp ( 48.54 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 57970
Comparison Time: 00:04:08 (hh:mm:ss) Elapsed Time, 1501 HSPs Collected
Number of families returned by RECON: 562
Round Time: 00:04:20 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 40667795


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40667795 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...
       536 repeats masked totaling 142311 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10635142 bp
       Num Contigs Represented = 148
       Non ambiguous bp:
             Initial: 10634257 bp
             After Masking: 10478546 bp
             Masked: 1.46 % 
 -- Input Database Coverage: 20667661 bp out of 20667795 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 64261
Comparison Time: 00:04:27 (hh:mm:ss) Elapsed Time, 1687 HSPs Collected
Number of families returned by RECON: 655
Round Time: 00:04:40 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 22 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.gt9ZX3/RM_539628.ThuSep110927262025
# 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: 00:09:32 (hh:mm:ss) Elapsed Time