RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.sUqoR1/RM_320784.FriSep121931292025
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: 1757730688
Database = /dev/shm/rModeler.sUqoR1/GCA_051397315.1_GA10_27 
  - Sequences = 193
  - Bases = 38494155
  - N50 = 658099
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2343548-2510908 |                                                   [ 1 ]
  2176188-2343547 |                                                   [  ]
  2008828-2176187 |                                                   [  ]
  1841468-2008827 |                                                   [  ]
  1674109-1841468 |                                                   [  ]
  1506749-1674108 |                                                   [  ]
  1339389-1506748 |                                                   [ 2 ]
  1172029-1339388 |                                                   [  ]
  1004669-1172028 |                                                   [ 2 ]
  837310-1004669  |*                                                  [ 5 ]
  669950-837309   |**                                                 [ 6 ]
  502590-669949   |***                                                [ 10 ]
  335230-502589   |******                                             [ 18 ]
  167870-335229   |*******                                            [ 20 ]
  511-167870      |************************************************** [ 129 ]

Storage Throughput = excellent ( 1706.62 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38494123 bp ( 38493615 non ambiguous )
   - Num Contigs Represented = 193
   - 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.. : 21 raw families identified
   - RepeatScout: Running filtering stage.. 20 families remaining
   - RepeatScout: 00:00:36 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:07 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:48 (hh:mm:ss) Elapsed Time : 18 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...
       201 repeats masked totaling 55597 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10001346 bp
       Num Contigs Represented = 95
       Non ambiguous bp:
             Initial: 10001171 bp
             After Masking: 9931372 bp
             Masked: 0.70 % 
 -- Input Database Coverage: 10001346 bp out of 38494155 bp ( 25.98 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 40186
Comparison Time: 00:03:47 (hh:mm:ss) Elapsed Time, 1737 HSPs Collected
Number of families returned by RECON: 733
Round Time: 00:03:56 (hh:mm:ss) Elapsed Time : 0 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       525 repeats masked totaling 140592 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28492697 bp
       Num Contigs Represented = 171
       Non ambiguous bp:
             Initial: 28492364 bp
             After Masking: 28312107 bp
             Masked: 0.63 % 
 -- Input Database Coverage: 38494043 bp out of 38494155 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 332520
Comparison Time: 00:14:36 (hh:mm:ss) Elapsed Time, 14241 HSPs Collected
Number of families returned by RECON: 3661
Round Time: 00:15:15 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.sUqoR1/RM_320784.FriSep121931292025
# 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: 00:20:06 (hh:mm:ss) Elapsed Time