RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.nXr6Rc/RM_1245174.FriSep120927142025
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: 1757694433
Database = /dev/shm/rModeler.nXr6Rc/GCA_040822295.1_ASM4082229v1 
  - Sequences = 13
  - Bases = 48623096
Storage Throughput = excellent ( 1692.21 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40025366 bp ( 40025366 non ambiguous )
   - Num Contigs Represented = 13
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 77 raw families identified
   - RepeatScout: Running filtering stage.. 62 families remaining
   - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 59 families... 00:11:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 2 satellite(s), 14 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:12:14 (hh:mm:ss) Elapsed Time : 43 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 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1011 repeats masked totaling 719343 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10012643 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 10012643 bp
             After Masking: 9281153 bp
             Masked: 7.31 % 
 -- Input Database Coverage: 10012643 bp out of 48623096 bp ( 20.59 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31125
Comparison Time: 00:04:02 (hh:mm:ss) Elapsed Time, 2285 HSPs Collected
Number of families returned by RECON: 608
Round Time: 00:09:22 (hh:mm:ss) Elapsed Time : 4 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2573 repeats masked totaling 2129108 bp(s).
   - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30012689 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 30012689 bp
             After Masking: 27842266 bp
             Masked: 7.23 % 
 -- Input Database Coverage: 40025332 bp out of 48623096 bp ( 82.32 % )
Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 285390
Comparison Time: 00:14:50 (hh:mm:ss) Elapsed Time, 13499 HSPs Collected
Number of families returned by RECON: 3208
Round Time: 00:18:33 (hh:mm:ss) Elapsed Time : 8 families discovered.
   - Increasing sample size to include end piece now = 98610453


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 98610453 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       930 repeats masked totaling 733038 bp(s).
   - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8597587 bp
       Num Contigs Represented = 12
       Non ambiguous bp:
             Initial: 8597587 bp
             After Masking: 7853278 bp
             Masked: 8.66 % 
 -- Input Database Coverage: 48622919 bp out of 48623096 bp ( 100.00 % )
Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 23005
Comparison Time: 00:02:48 (hh:mm:ss) Elapsed Time, 1161 HSPs Collected
Number of families returned by RECON: 507
Round Time: 00:03:30 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 55 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.nXr6Rc/RM_1245174.FriSep120927142025
# 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: 00:00:22 (hh:mm:ss) Elapsed Time


Program Time: 00:44:01 (hh:mm:ss) Elapsed Time