RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.3zvXr7/RM_1024384.MonSep81305342025
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: 1757361933
Database = /dev/shm/rModeler.3zvXr7/GCA_000966645.2_ASM96664v2 
  - Sequences = 22
  - Bases = 37018507
Storage Throughput = excellent ( 1690.03 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37018361 bp ( 37018361 non ambiguous )
   - Num Contigs Represented = 22
   - 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.. : 26 raw families identified
   - RepeatScout: Running filtering stage.. 18 families remaining
   - RepeatScout: 00:00:38 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:34 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:01:18 (hh:mm:ss) Elapsed Time : 16 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 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       197 repeats masked totaling 46131 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10021249 bp
       Num Contigs Represented = 16
       Non ambiguous bp:
             Initial: 10021249 bp
             After Masking: 9958555 bp
             Masked: 0.63 % 
 -- Input Database Coverage: 10021249 bp out of 37018507 bp ( 27.07 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32896
Comparison Time: 00:03:50 (hh:mm:ss) Elapsed Time, 30430 HSPs Collected
Number of families returned by RECON: 820
Round Time: 00:04:11 (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 : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       702 repeats masked totaling 180478 bp(s).
   - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26997032 bp
       Num Contigs Represented = 21
       Non ambiguous bp:
             Initial: 26997032 bp
             After Masking: 26764761 bp
             Masked: 0.86 % 
 -- Input Database Coverage: 37018281 bp out of 37018507 bp ( 100.00 % )
Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 230860
Comparison Time: 00:19:58 (hh:mm:ss) Elapsed Time, 185518 HSPs Collected
Number of families returned by RECON: 3379
Round Time: 02:25:28 (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.3zvXr7/RM_1024384.MonSep81305342025
# 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: 00:00:12 (hh:mm:ss) Elapsed Time


Program Time: 02:31:09 (hh:mm:ss) Elapsed Time