RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.QIGqDt/RM_266831.FriSep121858432025
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: 1757728723
Database = /dev/shm/rModeler.QIGqDt/GCA_051397125.1_GA10_19 
  - Sequences = 170
  - Bases = 38508892
  - N50 = 821719
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1658231-1776641 |                                                   [ 2 ]
  1539822-1658231 |                                                   [ 1 ]
  1421413-1539822 |                                                   [ 1 ]
  1303004-1421413 |*                                                  [ 3 ]
  1184595-1303004 |                                                   [  ]
  1066186-1184595 |                                                   [  ]
  947777-1066186  |*                                                  [ 3 ]
  829368-947777   |**                                                 [ 5 ]
  710959-829368   |*                                                  [ 4 ]
  592550-710959   |*                                                  [ 4 ]
  474141-592550   |***                                                [ 7 ]
  355732-474141   |***                                                [ 8 ]
  237323-355732   |******                                             [ 13 ]
  118914-237323   |******                                             [ 13 ]
  505-118914      |************************************************** [ 106 ]

Storage Throughput = excellent ( 1761.10 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38508786 bp ( 38508497 non ambiguous )
   - Num Contigs Represented = 170
   - 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.. : 22 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:08 (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: 00:00:49 (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 : 00:00:00 (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...
       192 repeats masked totaling 39688 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10021644 bp
       Num Contigs Represented = 87
       Non ambiguous bp:
             Initial: 10021558 bp
             After Masking: 9970260 bp
             Masked: 0.51 % 
 -- Input Database Coverage: 10021644 bp out of 38508892 bp ( 26.02 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 38226
Comparison Time: 00:03:45 (hh:mm:ss) Elapsed Time, 1805 HSPs Collected
Number of families returned by RECON: 748
Round Time: 00:03:56 (hh:mm:ss) Elapsed Time : 1 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...
       578 repeats masked totaling 162646 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28487062 bp
       Num Contigs Represented = 155
       Non ambiguous bp:
             Initial: 28486859 bp
             After Masking: 28279510 bp
             Masked: 0.73 % 
 -- Input Database Coverage: 38508706 bp out of 38508892 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 324415
Comparison Time: 00:14:30 (hh:mm:ss) Elapsed Time, 13266 HSPs Collected
Number of families returned by RECON: 3588
Round Time: 00:15:03 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 27 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.QIGqDt/RM_266831.FriSep121858432025
# 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: 00:19:55 (hh:mm:ss) Elapsed Time