RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.KWAfT9/RM_2139967.MonSep81751172025
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: 1757379077
Database = /dev/shm/rModeler.KWAfT9/GCA_002222475.1_Cryp_neof_Tu401_1_V1 
  - Sequences = 49
  - Bases = 18574041
Storage Throughput = excellent ( 1682.18 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18573918 bp ( 18232654 non ambiguous )
   - Num Contigs Represented = 49
   - 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.. : 39 raw families identified
   - RepeatScout: Running filtering stage.. 38 families remaining
   - RepeatScout: 00:00:16 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 37 families... 00:00:06 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 9 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:25 (hh:mm:ss) Elapsed Time : 28 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       377 repeats masked totaling 96438 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10178859 bp
       Num Contigs Represented = 43
       Non ambiguous bp:
             Initial: 10013553 bp
             After Masking: 9906710 bp
             Masked: 1.07 % 
 -- Input Database Coverage: 10178859 bp out of 18574041 bp ( 54.80 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 36585
Comparison Time: 00:03:42 (hh:mm:ss) Elapsed Time, 2405 HSPs Collected
Number of families returned by RECON: 708
Round Time: 00:03:54 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 38574041


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38574041 bp
   - Sequence extraction : 00:00:00 (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...
       453 repeats masked totaling 125676 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8394979 bp
       Num Contigs Represented = 38
       Non ambiguous bp:
             Initial: 8219021 bp
             After Masking: 8084441 bp
             Masked: 1.64 % 
 -- Input Database Coverage: 18573838 bp out of 18574041 bp ( 100.00 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 24310
Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 1934 HSPs Collected
Number of families returned by RECON: 523
Round Time: 00:03:03 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 31 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.KWAfT9/RM_2139967.MonSep81751172025
# 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: 00:07:29 (hh:mm:ss) Elapsed Time