RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.2F5Yn4/RM_3266137.ThuSep110930302025
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: 1757608229
Database = /dev/shm/rModeler.2F5Yn4/GCA_024399255.1_ASM2439925v1 
  - Sequences = 11
  - Bases = 2707802
Storage Throughput = excellent ( 1686.29 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 2707741 bp ( 2707741 non ambiguous )
   - Num Contigs Represented = 11
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 12, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 8 raw families identified
   - RepeatScout: Running filtering stage.. 8 families remaining
   - RepeatScout: 00:00:07 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 5 families... 00:03:53 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 3 satellite(s), 0 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:04:02 (hh:mm:ss) Elapsed Time : 2 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 00:00:03 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       171 repeats masked totaling 294970 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2707741 bp
       Num Contigs Represented = 11
       Non ambiguous bp:
             Initial: 2707741 bp
             After Masking: 2388427 bp
             Masked: 11.79 % 
 -- Input Database Coverage: 2707741 bp out of 2707802 bp ( 100.00 % )
Sampling Time: 00:00:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2701
Comparison Time: 00:00:50 (hh:mm:ss) Elapsed Time, 2878 HSPs Collected
Number of families returned by RECON: 142
Round Time: 00:01:30 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 3 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.2F5Yn4/RM_3266137.ThuSep110930302025
# 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: 00:00:09 (hh:mm:ss) Elapsed Time


Program Time: 00:05:41 (hh:mm:ss) Elapsed Time