RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.IJPYM1/RM_550841.MonSep81402432025
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: 1757365362
Database = /dev/shm/rModeler.IJPYM1/GCA_001599495.1_JCM_2005_assembly_v001 
  - Sequences = 56
  - Bases = 19606871
Storage Throughput = excellent ( 1687.68 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19606782 bp ( 19529975 non ambiguous )
   - Num Contigs Represented = 56
   - 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.. : 16 raw families identified
   - RepeatScout: Running filtering stage.. 16 families remaining
   - RepeatScout: 00:00:27 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 14 families... 00:00:05 (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: 00:00:35 (hh:mm:ss) Elapsed Time : 12 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       251 repeats masked totaling 48855 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10057337 bp
       Num Contigs Represented = 40
       Non ambiguous bp:
             Initial: 10013856 bp
             After Masking: 9904639 bp
             Masked: 1.09 % 
 -- Input Database Coverage: 10057337 bp out of 19606871 bp ( 51.29 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 36315
Comparison Time: 00:03:57 (hh:mm:ss) Elapsed Time, 16910 HSPs Collected
Number of families returned by RECON: 1554
Round Time: 00:04:32 (hh:mm:ss) Elapsed Time : 6 families discovered.
   - Increasing sample size to include end piece now = 39606871


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39606871 bp
   - Sequence extraction : 00:00:01 (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...
       3155 repeats masked totaling 312247 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9549365 bp
       Num Contigs Represented = 44
       Non ambiguous bp:
             Initial: 9516039 bp
             After Masking: 9139633 bp
             Masked: 3.96 % 
 -- Input Database Coverage: 19606702 bp out of 19606871 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32131
Comparison Time: 00:03:35 (hh:mm:ss) Elapsed Time, 2270 HSPs Collected
Number of families returned by RECON: 647
Round Time: 00:03:50 (hh:mm:ss) Elapsed Time : 3 families discovered.

RepeatScout/RECON discovery complete: 21 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.IJPYM1/RM_550841.MonSep81402432025
# 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: 00:09:03 (hh:mm:ss) Elapsed Time