RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.OX2Rg8/RM_3497950.SatSep130510002025
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: 1757765399
Database = /dev/shm/rModeler.OX2Rg8/GCA_927399515.3_gfLaeSulp1.3 
  - Sequences = 15
  - Bases = 37546112
Storage Throughput = excellent ( 1673.67 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37545976 bp ( 37545376 non ambiguous )
   - Num Contigs Represented = 15
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 196 raw families identified
   - RepeatScout: Running filtering stage.. 194 families remaining
   - RepeatScout: 00:01:06 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 187 families... 00:02:07 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 5 satellite(s), 53 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:03:18 (hh:mm:ss) Elapsed Time : 128 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2010 repeats masked totaling 1127102 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10000986 bp
       Num Contigs Represented = 15
       Non ambiguous bp:
             Initial: 10000786 bp
             After Masking: 8781463 bp
             Masked: 12.19 % 
 -- Input Database Coverage: 10000986 bp out of 37546112 bp ( 26.64 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31626
Comparison Time: 00:03:17 (hh:mm:ss) Elapsed Time, 7758 HSPs Collected
Number of families returned by RECON: 834
Round Time: 00:03:48 (hh:mm:ss) Elapsed Time : 6 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5208 repeats masked totaling 3307672 bp(s).
   - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27544960 bp
       Num Contigs Represented = 15
       Non ambiguous bp:
             Initial: 27544560 bp
             After Masking: 24159195 bp
             Masked: 12.29 % 
 -- Input Database Coverage: 37545946 bp out of 37546112 bp ( 100.00 % )
Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 241165
Comparison Time: 00:12:26 (hh:mm:ss) Elapsed Time, 21043 HSPs Collected
Number of families returned by RECON: 3297
Round Time: 00:13:15 (hh:mm:ss) Elapsed Time : 18 families discovered.

RepeatScout/RECON discovery complete: 152 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.OX2Rg8/RM_3497950.SatSep130510002025
# 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: 00:00:38 (hh:mm:ss) Elapsed Time


Program Time: 00:20:59 (hh:mm:ss) Elapsed Time