RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.f6LjrY/RM_236377.TueSep90502492025
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: 1757419368
Database = /dev/shm/rModeler.f6LjrY/GCA_008062615.2_ASM806261v2 
  - Sequences = 51
  - Bases = 10651449
Storage Throughput = excellent ( 1667.79 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 10651336 bp ( 10642693 non ambiguous )
   - Num Contigs Represented = 51
   - 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.. : 11 raw families identified
   - RepeatScout: Running filtering stage.. 8 families remaining
   - RepeatScout: 00:00:10 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 7 families... 00:00:07 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:19 (hh:mm:ss) Elapsed Time : 4 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...
       122 repeats masked totaling 59564 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10047290 bp
       Num Contigs Represented = 47
       Non ambiguous bp:
             Initial: 10039879 bp
             After Masking: 9940021 bp
             Masked: 0.99 % 
 -- Input Database Coverage: 10047290 bp out of 10651449 bp ( 94.33 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 41905
Comparison Time: 00:04:13 (hh:mm:ss) Elapsed Time, 4795 HSPs Collected
Number of families returned by RECON: 1001
Round Time: 00:04:30 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 30651449


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30651449 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       23 repeats masked totaling 7226 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 603966 bp
       Num Contigs Represented = 11
       Non ambiguous bp:
             Initial: 602734 bp
             After Masking: 592544 bp
             Masked: 1.69 % 
 -- Input Database Coverage: 10651256 bp out of 10651449 bp ( 100.00 % )
Sampling Time: 00:00:02 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 171
Comparison Time: 00:00:11 (hh:mm:ss) Elapsed Time, 19 HSPs Collected
Number of families returned by RECON: 15
Round Time: 00:00:13 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 6 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.f6LjrY/RM_236377.TueSep90502492025
# 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: 00:05:08 (hh:mm:ss) Elapsed Time