RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.Mgwocv/RM_566729.ThuFeb120031442026
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: 1770885104
Database = /dev/shm/rModeler.Mgwocv/GCA_001306245.1_ASM130624v1 
  - Sequences = 18
  - Bases = 9221024
Storage Throughput = excellent ( 1780.72 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 9220944 bp ( 8975185 non ambiguous )
   - Num Contigs Represented = 18
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 2 raw families identified
   - RepeatScout: Running filtering stage.. 1 families remaining
   - RepeatScout: 00:00:33 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 1 families... 00:00:03 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:00 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:00 (hh:mm:ss) Elapsed Time
Round Time: 00:00:37 (hh:mm:ss) Elapsed Time : 1 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       15 repeats masked totaling 9257 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9220944 bp
       Num Contigs Represented = 18
       Non ambiguous bp:
             Initial: 8975185 bp
             After Masking: 8898035 bp
             Masked: 0.86 % 
 -- Input Database Coverage: 9220944 bp out of 9221024 bp ( 100.00 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 28441
Comparison Time: 00:04:10 (hh:mm:ss) Elapsed Time, 1014 HSPs Collected
Number of families returned by RECON: 341
Round Time: 00:04:33 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 2 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.Mgwocv/RM_566729.ThuFeb120031442026
# 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: 00:05:15 (hh:mm:ss) Elapsed Time