RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.VuLkmp/RM_52826.WedSep101415402025
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: 1757538939
Database = /dev/shm/rModeler.VuLkmp/GCA_018154595.1_ASM1815459v1 
  - Sequences = 343
  - Bases = 19511902
  - N50 = 490615
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1468715-1573609 |                                                   [ 1 ]
  1363821-1468714 |                                                   [  ]
  1258927-1363820 |                                                   [  ]
  1154033-1258926 |                                                   [  ]
  1049139-1154032 |                                                   [  ]
  944245-1049138  |                                                   [ 2 ]
  839351-944244   |                                                   [  ]
  734457-839350   |                                                   [  ]
  629563-734456   |                                                   [ 1 ]
  524669-629562   |*                                                  [ 7 ]
  419775-524668   |*                                                  [ 6 ]
  314881-419774   |                                                   [ 3 ]
  209987-314880   |**                                                 [ 12 ]
  105093-209986   |***                                                [ 19 ]
  200-105093      |************************************************** [ 292 ]

Storage Throughput = excellent ( 1527.86 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19511837 bp ( 19504872 non ambiguous )
   - Num Contigs Represented = 343
   - 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.. : 17 raw families identified
   - RepeatScout: Running filtering stage.. 17 families remaining
   - RepeatScout: 00:00:26 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 16 families... 00:00:05 (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: 00:00:34 (hh:mm:ss) Elapsed Time : 13 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       310 repeats masked totaling 53122 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10018910 bp
       Num Contigs Represented = 207
       Non ambiguous bp:
             Initial: 10015264 bp
             After Masking: 9906890 bp
             Masked: 1.08 % 
 -- Input Database Coverage: 10018910 bp out of 19511902 bp ( 51.35 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 83436
Comparison Time: 00:04:45 (hh:mm:ss) Elapsed Time, 18752 HSPs Collected
Number of families returned by RECON: 1671
Round Time: 00:05:20 (hh:mm:ss) Elapsed Time : 6 families discovered.
   - Increasing sample size to include end piece now = 39511902


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39511902 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2717 repeats masked totaling 274969 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9492847 bp
       Num Contigs Represented = 191
       Non ambiguous bp:
             Initial: 9489528 bp
             After Masking: 9159742 bp
             Masked: 3.48 % 
 -- Input Database Coverage: 19511757 bp out of 19511902 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 70876
Comparison Time: 00:04:24 (hh:mm:ss) Elapsed Time, 2529 HSPs Collected
Number of families returned by RECON: 685
Round Time: 00:04:39 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 21 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.VuLkmp/RM_52826.WedSep101415402025
# 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: 00:10:39 (hh:mm:ss) Elapsed Time