RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.BS6cKu/RM_674721.ThuFeb121002552026
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: 1770919375
Database = /dev/shm/rModeler.BS6cKu/GCA_019332025.1_ASM1933202v1 
  - Sequences = 7
  - Bases = 12589091
Storage Throughput = excellent ( 1642.75 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12588990 bp ( 12588990 non ambiguous )
   - Num Contigs Represented = 7
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 11 raw families identified
   - RepeatScout: Running filtering stage.. 11 families remaining
   - RepeatScout: 00:00:13 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 10 families... 00:00:05 (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: 00:00:20 (hh:mm:ss) Elapsed Time : 9 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...
       263 repeats masked totaling 48721 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10030070 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 10030070 bp
             After Masking: 9943661 bp
             Masked: 0.86 % 
 -- Input Database Coverage: 10030070 bp out of 12589091 bp ( 79.67 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31878
Comparison Time: 00:03:12 (hh:mm:ss) Elapsed Time, 3314 HSPs Collected
Number of families returned by RECON: 851
Round Time: 00:03:28 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 32589091


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32589091 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       44 repeats masked totaling 14781 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2558887 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 2558887 bp
             After Masking: 2539627 bp
             Masked: 0.75 % 
 -- Input Database Coverage: 12588957 bp out of 12589091 bp ( 100.00 % )
Sampling Time: 00:00:03 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2080
Comparison Time: 00:00:38 (hh:mm:ss) Elapsed Time, 198 HSPs Collected
Number of families returned by RECON: 94
Round Time: 00:00:41 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 11 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.BS6cKu/RM_674721.ThuFeb121002552026
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:04:35 (hh:mm:ss) Elapsed Time