RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.vrgyw7/RM_148835.WedSep101748092025
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: 1757551689
Database = /dev/shm/rModeler.vrgyw7/GCA_019054715.1_ASM1905471v1 
  - Sequences = 124
  - Bases = 39283611
  - N50 = 842526
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1866968-1999658 |                                                   [ 1 ]
  1734279-1866968 |                                                   [ 1 ]
  1601590-1734279 |                                                   [  ]
  1468901-1601590 |                                                   [  ]
  1336212-1468901 |                                                   [ 1 ]
  1203523-1336212 |                                                   [ 1 ]
  1070834-1203523 |**                                                 [ 4 ]
  938145-1070834  |                                                   [ 1 ]
  805456-938145   |******                                             [ 9 ]
  672767-805456   |**                                                 [ 4 ]
  540078-672767   |*****                                              [ 8 ]
  407389-540078   |*****                                              [ 7 ]
  274700-407389   |*****                                              [ 8 ]
  142011-274700   |******                                             [ 9 ]
  9322-142011     |************************************************** [ 70 ]

Storage Throughput = excellent ( 1473.02 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39283511 bp ( 39283022 non ambiguous )
   - Num Contigs Represented = 124
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 35 raw families identified
   - RepeatScout: Running filtering stage.. 35 families remaining
   - RepeatScout: 00:00:43 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 33 families... 00:00:16 (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: 00:01:04 (hh:mm:ss) Elapsed Time : 31 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       724 repeats masked totaling 180923 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10018863 bp
       Num Contigs Represented = 78
       Non ambiguous bp:
             Initial: 10018568 bp
             After Masking: 9817972 bp
             Masked: 2.00 % 
 -- Input Database Coverage: 10018863 bp out of 39283611 bp ( 25.50 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 34980
Comparison Time: 00:03:33 (hh:mm:ss) Elapsed Time, 1892 HSPs Collected
Number of families returned by RECON: 643
Round Time: 00:03:46 (hh:mm:ss) Elapsed Time : 3 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2281 repeats masked totaling 510126 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29264568 bp
       Num Contigs Represented = 114
       Non ambiguous bp:
             Initial: 29264374 bp
             After Masking: 28701862 bp
             Masked: 1.92 % 
 -- Input Database Coverage: 39283431 bp out of 39283611 bp ( 100.00 % )
Sampling Time: 00:00:23 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 300700
Comparison Time: 00:14:48 (hh:mm:ss) Elapsed Time, 12901 HSPs Collected
Number of families returned by RECON: 3482
Round Time: 00:15:25 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 42 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.vrgyw7/RM_148835.WedSep101748092025
# 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: 00:20:24 (hh:mm:ss) Elapsed Time