RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.sSzzep/RM_537558.FriSep120301282025
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: 1757671287
Database = /dev/shm/rModeler.sSzzep/GCA_032248835.1_ASM3224883v1 
  - Sequences = 8
  - Bases = 31915525
Storage Throughput = excellent ( 1699.89 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 31915366 bp ( 31900929 non ambiguous )
   - Num Contigs Represented = 8
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 20 raw families identified
   - RepeatScout: Running filtering stage.. 11 families remaining
   - RepeatScout: 00:00:50 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 11 families... 00:00:36 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 4 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:01:32 (hh:mm:ss) Elapsed Time : 6 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 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       60 repeats masked totaling 8388 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10009439 bp
       Num Contigs Represented = 8
       Non ambiguous bp:
             Initial: 10004849 bp
             After Masking: 9954245 bp
             Masked: 0.51 % 
 -- Input Database Coverage: 10009439 bp out of 31915525 bp ( 31.36 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31626
Comparison Time: 00:04:04 (hh:mm:ss) Elapsed Time, 1947 HSPs Collected
Number of families returned by RECON: 676
Round Time: 00:04:29 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       808 repeats masked totaling 112274 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 21905847 bp
       Num Contigs Represented = 8
       Non ambiguous bp:
             Initial: 21896000 bp
             After Masking: 21675834 bp
             Masked: 1.01 % 
 -- Input Database Coverage: 31915286 bp out of 31915525 bp ( 100.00 % )
Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 150975
Comparison Time: 00:11:54 (hh:mm:ss) Elapsed Time, 16376 HSPs Collected
Number of families returned by RECON: 2162
Round Time: 00:13:08 (hh:mm:ss) Elapsed Time : 6 families discovered.

RepeatScout/RECON discovery complete: 14 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.sSzzep/RM_537558.FriSep120301282025
# 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: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:19:17 (hh:mm:ss) Elapsed Time