RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.1QW1u6/RM_1581981.WedSep101750222025
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: 1757551821
Database = /dev/shm/rModeler.1QW1u6/GCA_019054735.1_ASM1905473v1 
  - Sequences = 47
  - Bases = 39376409
Storage Throughput = excellent ( 1536.96 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39376321 bp ( 39375547 non ambiguous )
   - Num Contigs Represented = 47
   - 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.. : 39 raw families identified
   - RepeatScout: Running filtering stage.. 27 families remaining
   - RepeatScout: 00:00:42 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 26 families... 00:00:09 (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: 00:00:55 (hh:mm:ss) Elapsed Time : 23 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...
       624 repeats masked totaling 89641 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10037065 bp
       Num Contigs Represented = 28
       Non ambiguous bp:
             Initial: 10036869 bp
             After Masking: 9931754 bp
             Masked: 1.05 % 
 -- Input Database Coverage: 10037065 bp out of 39376409 bp ( 25.49 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32385
Comparison Time: 00:03:41 (hh:mm:ss) Elapsed Time, 1907 HSPs Collected
Number of families returned by RECON: 650
Round Time: 00:03:55 (hh:mm:ss) Elapsed Time : 0 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1965 repeats masked totaling 381374 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29339176 bp
       Num Contigs Represented = 42
       Non ambiguous bp:
             Initial: 29338598 bp
             After Masking: 28916242 bp
             Masked: 1.44 % 
 -- Input Database Coverage: 39376241 bp out of 39376409 bp ( 100.00 % )
Sampling Time: 00:00:26 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 283128
Comparison Time: 00:17:31 (hh:mm:ss) Elapsed Time, 19744 HSPs Collected
Number of families returned by RECON: 3486
Round Time: 00:29:15 (hh:mm:ss) Elapsed Time : 14 families discovered.

RepeatScout/RECON discovery complete: 37 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.1QW1u6/RM_1581981.WedSep101750222025
# 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: 00:00:10 (hh:mm:ss) Elapsed Time


Program Time: 00:34:15 (hh:mm:ss) Elapsed Time