RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.4FhjZz/RM_539418.MonSep81016122025
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: 1757351772
Database = /dev/shm/rModeler.4FhjZz/GCA_000149245.3_CNA3 
  - Sequences = 15
  - Bases = 18916112
Storage Throughput = excellent ( 1144.05 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18916068 bp ( 18915608 non ambiguous )
   - Num Contigs Represented = 15
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 48 raw families identified
   - RepeatScout: Running filtering stage.. 47 families remaining
   - RepeatScout: 00:00:41 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 45 families... 00:00:40 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:01:29 (hh:mm:ss) Elapsed Time : 41 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       827 repeats masked totaling 535014 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10026021 bp
       Num Contigs Represented = 14
       Non ambiguous bp:
             Initial: 10025734 bp
             After Masking: 9480179 bp
             Masked: 5.44 % 
 -- Input Database Coverage: 10026021 bp out of 18916112 bp ( 53.00 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31878
Comparison Time: 00:05:50 (hh:mm:ss) Elapsed Time, 1877 HSPs Collected
Number of families returned by RECON: 603
Round Time: 00:06:20 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 38916112


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38916112 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       723 repeats masked totaling 357198 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8889967 bp
       Num Contigs Represented = 15
       Non ambiguous bp:
             Initial: 8889794 bp
             After Masking: 8522546 bp
             Masked: 4.13 % 
 -- Input Database Coverage: 18915988 bp out of 18916112 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 25651
Comparison Time: 00:04:30 (hh:mm:ss) Elapsed Time, 1351 HSPs Collected
Number of families returned by RECON: 541
Round Time: 00:04:50 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 43 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.4FhjZz/RM_539418.MonSep81016122025
# 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: 00:00:35 (hh:mm:ss) Elapsed Time


Program Time: 00:13:14 (hh:mm:ss) Elapsed Time