RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.Qt7E71/RM_2804660.MonSep81729042025
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: 1757377743
Database = /dev/shm/rModeler.Qt7E71/GCA_002221985.1_Cryp_neof_grubii_A1-35-8_V1 
  - Sequences = 557
  - Bases = 18819906
  - N50 = 160092
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  419877-449797 |                                                   [ 1 ]
  389957-419876 |                                                   [ 1 ]
  360037-389956 |                                                   [  ]
  330117-360036 |                                                   [ 3 ]
  300198-330117 |                                                   [ 4 ]
  270278-300197 |                                                   [ 2 ]
  240358-270277 |                                                   [ 4 ]
  210438-240357 |                                                   [ 5 ]
  180518-210437 |*                                                  [ 10 ]
  150599-180518 |*                                                  [ 11 ]
  120679-150598 |*                                                  [ 12 ]
  90759-120678  |**                                                 [ 21 ]
  60839-90758   |***                                                [ 30 ]
  30919-60838   |****                                               [ 40 ]
  1000-30919    |************************************************** [ 413 ]

Storage Throughput = excellent ( 1676.24 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18819809 bp ( 18819099 non ambiguous )
   - Num Contigs Represented = 557
   - 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: 00:00:16 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 21 families... 00:00:17 (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: 00:00:36 (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 : 00:00:00 (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...
       250 repeats masked totaling 62665 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10008737 bp
       Num Contigs Represented = 336
       Non ambiguous bp:
             Initial: 10008482 bp
             After Masking: 9936453 bp
             Masked: 0.72 % 
 -- Input Database Coverage: 10008737 bp out of 18819906 bp ( 53.18 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 115921
Comparison Time: 00:04:44 (hh:mm:ss) Elapsed Time, 2686 HSPs Collected
Number of families returned by RECON: 726
Round Time: 00:04:59 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 38819906


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38819906 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...
       360 repeats masked totaling 85785 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8810992 bp
       Num Contigs Represented = 318
       Non ambiguous bp:
             Initial: 8810537 bp
             After Masking: 8715169 bp
             Masked: 1.08 % 
 -- Input Database Coverage: 18819729 bp out of 18819906 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 97461
Comparison Time: 00:04:12 (hh:mm:ss) Elapsed Time, 1660 HSPs Collected
Number of families returned by RECON: 610
Round Time: 00:04:21 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 22 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.Qt7E71/RM_2804660.MonSep81729042025
# 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: 00:10:02 (hh:mm:ss) Elapsed Time