RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.bKJ1Qd/RM_2226150.WedOct291127102025
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: 1761762429
Database = /dev/shm/rModeler.bKJ1Qd/GCA_016808195.1_ASM1680819v1 
  - Sequences = 8
  - Bases = 38569175
Storage Throughput = excellent ( 1125.24 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38569059 bp ( 38563866 non ambiguous )
   - Num Contigs Represented = 8
   - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 77 raw families identified
   - RepeatScout: Running filtering stage.. 68 families remaining
   - RepeatScout: 00:02:25 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 68 families... 00:06:27 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 5 satellite(s), 15 contained, found in 00:00:04 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:04 (hh:mm:ss) Elapsed Time
Round Time: 00:09:13 (hh:mm:ss) Elapsed Time : 48 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       846 repeats masked totaling 603900 bp(s).
   - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10032566 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 10028245 bp
             After Masking: 9349280 bp
             Masked: 6.77 % 
 -- Input Database Coverage: 10032566 bp out of 38569175 bp ( 26.01 % )
Sampling Time: 00:00:44 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32131
Comparison Time: 00:05:12 (hh:mm:ss) Elapsed Time, 1596 HSPs Collected
Number of families returned by RECON: 615
Round Time: 00:06:04 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3174 repeats masked totaling 1898373 bp(s).
   - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28536451 bp
       Num Contigs Represented = 8
       Non ambiguous bp:
             Initial: 28535579 bp
             After Masking: 26454725 bp
             Masked: 7.29 % 
 -- Input Database Coverage: 38569017 bp out of 38569175 bp ( 100.00 % )
Sampling Time: 00:01:44 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 255255
Comparison Time: 00:27:07 (hh:mm:ss) Elapsed Time, 9856 HSPs Collected
Number of families returned by RECON: 2780
Round Time: 00:30:28 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 57 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.bKJ1Qd/RM_2226150.WedOct291127102025
# 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: 00:00:55 (hh:mm:ss) Elapsed Time


Program Time: 00:46:40 (hh:mm:ss) Elapsed Time