RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.iwxS88/RM_2218512.WedSep101758102025
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: 1757552290
Database = /dev/shm/rModeler.iwxS88/GCA_019054865.1_ASM1905486v1 
  - Sequences = 53
  - Bases = 36558494
Storage Throughput = excellent ( 1627.50 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36558400 bp ( 36558291 non ambiguous )
   - Num Contigs Represented = 53
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 19 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:36 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 16 families... 00:00:06 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:00 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:00 (hh:mm:ss) Elapsed Time
Round Time: 00:00:46 (hh:mm:ss) Elapsed Time : 15 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...
       502 repeats masked totaling 67771 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10036156 bp
       Num Contigs Represented = 50
       Non ambiguous bp:
             Initial: 10036156 bp
             After Masking: 9954531 bp
             Masked: 0.81 % 
 -- Input Database Coverage: 10036156 bp out of 36558494 bp ( 27.45 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33411
Comparison Time: 00:03:31 (hh:mm:ss) Elapsed Time, 1652 HSPs Collected
Number of families returned by RECON: 565
Round Time: 00:03:44 (hh:mm:ss) Elapsed Time : 3 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1689 repeats masked totaling 250063 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26522219 bp
       Num Contigs Represented = 53
       Non ambiguous bp:
             Initial: 26522110 bp
             After Masking: 26242420 bp
             Masked: 1.05 % 
 -- Input Database Coverage: 36558375 bp out of 36558494 bp ( 100.00 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 233586
Comparison Time: 00:12:43 (hh:mm:ss) Elapsed Time, 9441 HSPs Collected
Number of families returned by RECON: 2757
Round Time: 00:13:16 (hh:mm:ss) Elapsed Time : 7 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.iwxS88/RM_2218512.WedSep101758102025
# 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: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:17:53 (hh:mm:ss) Elapsed Time