RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.mVzIMJ/RM_3484788.WedSep101216442025
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: 1757531804
Database = /dev/shm/rModeler.mVzIMJ/GCA_017315405.1_ASM1731540v1 
  - Sequences = 16
  - Bases = 14526448
Storage Throughput = excellent ( 1584.30 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14526387 bp ( 14486356 non ambiguous )
   - Num Contigs Represented = 16
   - 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.. : 30 raw families identified
   - RepeatScout: Running filtering stage.. 27 families remaining
   - RepeatScout: 00:01:01 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 26 families... 00:00:19 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:23 (hh:mm:ss) Elapsed Time : 24 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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       331 repeats masked totaling 190177 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10037812 bp
       Num Contigs Represented = 14
       Non ambiguous bp:
             Initial: 10008635 bp
             After Masking: 9711399 bp
             Masked: 2.97 % 
 -- Input Database Coverage: 10037812 bp out of 14526448 bp ( 69.10 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33670
Comparison Time: 00:05:22 (hh:mm:ss) Elapsed Time, 3315 HSPs Collected
Number of families returned by RECON: 937
Round Time: 00:05:49 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 34526448


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34526448 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...
       212 repeats masked totaling 92919 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4488530 bp
       Num Contigs Represented = 12
       Non ambiguous bp:
             Initial: 4477676 bp
             After Masking: 4334806 bp
             Masked: 3.19 % 
 -- Input Database Coverage: 14526342 bp out of 14526448 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 6328
Comparison Time: 00:01:43 (hh:mm:ss) Elapsed Time, 779 HSPs Collected
Number of families returned by RECON: 260
Round Time: 00:01:52 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.mVzIMJ/RM_3484788.WedSep101216442025
# 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: 00:09:11 (hh:mm:ss) Elapsed Time