RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.5S08X2/RM_3046349.ThuSep110842562025
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: 1757605375
Database = /dev/shm/rModeler.5S08X2/GCA_024220415.1_ASM2422041v1 
  - Sequences = 20
  - Bases = 14826637
Storage Throughput = excellent ( 1725.27 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14826519 bp ( 14826419 non ambiguous )
   - Num Contigs Represented = 20
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 41 raw families identified
   - RepeatScout: Running filtering stage.. 34 families remaining
   - RepeatScout: 00:01:04 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 30 families... 00:00:16 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 6 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:22 (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 : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       315 repeats masked totaling 158164 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10020582 bp
       Num Contigs Represented = 15
       Non ambiguous bp:
             Initial: 10020582 bp
             After Masking: 9724461 bp
             Masked: 2.96 % 
 -- Input Database Coverage: 10020582 bp out of 14826637 bp ( 67.58 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33153
Comparison Time: 00:05:13 (hh:mm:ss) Elapsed Time, 3661 HSPs Collected
Number of families returned by RECON: 926
Round Time: 00:05:43 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 34826637


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34826637 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       201 repeats masked totaling 120855 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4805860 bp
       Num Contigs Represented = 19
       Non ambiguous bp:
             Initial: 4805760 bp
             After Masking: 4608505 bp
             Masked: 4.10 % 
 -- Input Database Coverage: 14826442 bp out of 14826637 bp ( 100.00 % )
Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 7503
Comparison Time: 00:03:05 (hh:mm:ss) Elapsed Time, 757 HSPs Collected
Number of families returned by RECON: 237
Round Time: 00:03:27 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.5S08X2/RM_3046349.ThuSep110842562025
# 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: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:10:40 (hh:mm:ss) Elapsed Time