RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.7qPLJb/RM_3917594.MonSep81056292025
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: 1757354188
Database = /dev/shm/rModeler.7qPLJb/GCA_000328475.2_Umaydis521_2.0 
  - Sequences = 27
  - Bases = 19664356
Storage Throughput = excellent ( 1656.12 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19664258 bp ( 19641558 non ambiguous )
   - Num Contigs Represented = 27
   - 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.. : 22 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:00:28 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 20 families... 00:00:43 (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: 00:01:14 (hh:mm:ss) Elapsed Time : 19 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...
       694 repeats masked totaling 187788 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10028430 bp
       Num Contigs Represented = 25
       Non ambiguous bp:
             Initial: 10016930 bp
             After Masking: 9763271 bp
             Masked: 2.53 % 
 -- Input Database Coverage: 10028430 bp out of 19664356 bp ( 51.00 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33930
Comparison Time: 00:03:51 (hh:mm:ss) Elapsed Time, 9347 HSPs Collected
Number of families returned by RECON: 1257
Round Time: 00:04:14 (hh:mm:ss) Elapsed Time : 8 families discovered.
   - Increasing sample size to include end piece now = 39664356


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39664356 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...
       2842 repeats masked totaling 366901 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9635748 bp
       Num Contigs Represented = 25
       Non ambiguous bp:
             Initial: 9624548 bp
             After Masking: 9199584 bp
             Masked: 4.42 % 
 -- Input Database Coverage: 19664178 bp out of 19664356 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 30381
Comparison Time: 00:03:46 (hh:mm:ss) Elapsed Time, 1357 HSPs Collected
Number of families returned by RECON: 624
Round Time: 00:03:56 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 27 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.7qPLJb/RM_3917594.MonSep81056292025
# 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: 00:00:09 (hh:mm:ss) Elapsed Time


Program Time: 00:09:33 (hh:mm:ss) Elapsed Time