RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.3JXmcG/RM_913776.MonSep81559242025
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: 1757372363
Database = /dev/shm/rModeler.3JXmcG/GCA_001703955.2_RBG5266v2 
  - Sequences = 77
  - Bases = 36341670
Storage Throughput = excellent ( 1055.77 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36341578 bp ( 36275778 non ambiguous )
   - Num Contigs Represented = 77
   - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 32 raw families identified
   - RepeatScout: Running filtering stage.. 17 families remaining
   - RepeatScout: 00:00:57 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 17 families... 00:00:07 (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: 00:01:22 (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 : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       219 repeats masked totaling 28065 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10050883 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 10031583 bp
             After Masking: 9989121 bp
             Masked: 0.42 % 
 -- Input Database Coverage: 10050883 bp out of 36341670 bp ( 27.66 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 34191
Comparison Time: 00:05:52 (hh:mm:ss) Elapsed Time, 36094 HSPs Collected
Number of families returned by RECON: 936
Round Time: 00:06:45 (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 : 00:00:10 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       716 repeats masked totaling 80661 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26290615 bp
       Num Contigs Represented = 68
       Non ambiguous bp:
             Initial: 26244115 bp
             After Masking: 26133806 bp
             Masked: 0.42 % 
 -- Input Database Coverage: 36341498 bp out of 36341670 bp ( 100.00 % )
Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 256686
Comparison Time: 00:25:52 (hh:mm:ss) Elapsed Time, 178710 HSPs Collected
Number of families returned by RECON: 3269
Round Time: 00:31:56 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.3JXmcG/RM_913776.MonSep81559242025
# 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: 00:00:13 (hh:mm:ss) Elapsed Time


Program Time: 00:40:16 (hh:mm:ss) Elapsed Time