RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.tONCjL/RM_672163.WedSep101359232025
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: 1757537962
Database = /dev/shm/rModeler.tONCjL/GCA_018154185.1_ASM1815418v1 
  - Sequences = 421
  - Bases = 19619605
  - N50 = 507673
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1098458-1176905 |                                                   [ 1 ]
  1020011-1098458 |                                                   [ 1 ]
  941564-1020011  |                                                   [ 1 ]
  863117-941564   |                                                   [ 1 ]
  784670-863117   |                                                   [ 1 ]
  706223-784670   |                                                   [  ]
  627776-706223   |                                                   [ 1 ]
  549329-627776   |                                                   [ 4 ]
  470882-549329   |                                                   [ 7 ]
  392435-470882   |                                                   [ 4 ]
  313988-392435   |                                                   [ 2 ]
  235541-313988   |                                                   [ 5 ]
  157094-235541   |                                                   [ 7 ]
  78647-157094    |*                                                  [ 12 ]
  200-78647       |************************************************** [ 374 ]

Storage Throughput = excellent ( 1622.46 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19619564 bp ( 19614230 non ambiguous )
   - Num Contigs Represented = 421
   - 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.. : 24 raw families identified
   - RepeatScout: Running filtering stage.. 23 families remaining
   - RepeatScout: 00:00:27 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 22 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 5 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 : 17 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       330 repeats masked totaling 55026 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10029075 bp
       Num Contigs Represented = 240
       Non ambiguous bp:
             Initial: 10026366 bp
             After Masking: 9916759 bp
             Masked: 1.09 % 
 -- Input Database Coverage: 10029075 bp out of 19619605 bp ( 51.12 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 99681
Comparison Time: 00:04:52 (hh:mm:ss) Elapsed Time, 20305 HSPs Collected
Number of families returned by RECON: 1634
Round Time: 00:05:34 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 39619605


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39619605 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...
       2396 repeats masked totaling 239792 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9590427 bp
       Num Contigs Represented = 233
       Non ambiguous bp:
             Initial: 9587802 bp
             After Masking: 9296959 bp
             Masked: 3.03 % 
 -- Input Database Coverage: 19619502 bp out of 19619605 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 88410
Comparison Time: 00:04:38 (hh:mm:ss) Elapsed Time, 3028 HSPs Collected
Number of families returned by RECON: 815
Round Time: 00:04:53 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 19 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.tONCjL/RM_672163.WedSep101359232025
# 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: 00:00:05 (hh:mm:ss) Elapsed Time


Program Time: 00:11:06 (hh:mm:ss) Elapsed Time