RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.GsY6Y1/RM_2747937.MonSep81848552025
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: 1757382534
Database = /dev/shm/rModeler.GsY6Y1/GCA_002352725.1_FGRA07 
  - Sequences = 67
  - Bases = 36883775
Storage Throughput = excellent ( 1675.00 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36883648 bp ( 36883222 non ambiguous )
   - Num Contigs Represented = 67
   - 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.. : 24 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:39 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 19 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:48 (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...
       208 repeats masked totaling 28252 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10021595 bp
       Num Contigs Represented = 39
       Non ambiguous bp:
             Initial: 10021559 bp
             After Masking: 9971754 bp
             Masked: 0.50 % 
 -- Input Database Coverage: 10021595 bp out of 36883775 bp ( 27.17 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33930
Comparison Time: 00:03:59 (hh:mm:ss) Elapsed Time, 28478 HSPs Collected
Number of families returned by RECON: 833
Round Time: 00:06:08 (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 : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       625 repeats masked totaling 105114 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26862028 bp
       Num Contigs Represented = 60
       Non ambiguous bp:
             Initial: 26861638 bp
             After Masking: 26722076 bp
             Masked: 0.52 % 
 -- Input Database Coverage: 36883623 bp out of 36883775 bp ( 100.00 % )
Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 247456
Comparison Time: 00:14:23 (hh:mm:ss) Elapsed Time, 187679 HSPs Collected
Number of families returned by RECON: 3434
Round Time: 00:16:13 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.GsY6Y1/RM_2747937.MonSep81848552025
# 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: 00:23:15 (hh:mm:ss) Elapsed Time