RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.SWQ1QT/RM_1403796.FriSep122034262025
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: 1757734465
Database = /dev/shm/rModeler.SWQ1QT/GCA_051397695.1_GA10_4 
  - Sequences = 232
  - Bases = 38413709
  - N50 = 519736
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1884212-2018763 |                                                   [ 1 ]
  1749662-1884212 |                                                   [  ]
  1615112-1749662 |                                                   [ 1 ]
  1480562-1615112 |                                                   [  ]
  1346012-1480562 |                                                   [ 1 ]
  1211461-1346011 |                                                   [  ]
  1076911-1211461 |                                                   [  ]
  942361-1076911  |*                                                  [ 5 ]
  807811-942361   |                                                   [ 1 ]
  673261-807811   |*                                                  [ 6 ]
  538710-673260   |*                                                  [ 4 ]
  404160-538710   |***                                                [ 11 ]
  269610-404160   |******                                             [ 21 ]
  135060-269610   |*******                                            [ 24 ]
  510-135060      |************************************************** [ 157 ]

Storage Throughput = excellent ( 1653.86 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38413595 bp ( 38413067 non ambiguous )
   - Num Contigs Represented = 232
   - 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.. : 23 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:00:36 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 20 families... 00:00:04 (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: 00:00:45 (hh:mm:ss) Elapsed Time : 20 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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       158 repeats masked totaling 23805 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10039046 bp
       Num Contigs Represented = 118
       Non ambiguous bp:
             Initial: 10038908 bp
             After Masking: 10000322 bp
             Masked: 0.38 % 
 -- Input Database Coverage: 10039046 bp out of 38413709 bp ( 26.13 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 41905
Comparison Time: 00:04:11 (hh:mm:ss) Elapsed Time, 1611 HSPs Collected
Number of families returned by RECON: 719
Round Time: 00:04:26 (hh:mm:ss) Elapsed Time : 2 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 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       639 repeats masked totaling 112381 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28374469 bp
       Num Contigs Represented = 199
       Non ambiguous bp:
             Initial: 28374079 bp
             After Masking: 28223068 bp
             Masked: 0.53 % 
 -- Input Database Coverage: 38413515 bp out of 38413709 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 346528
Comparison Time: 00:14:40 (hh:mm:ss) Elapsed Time, 13601 HSPs Collected
Number of families returned by RECON: 3591
Round Time: 00:15:18 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 32 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.SWQ1QT/RM_1403796.FriSep122034262025
# 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: 00:20:36 (hh:mm:ss) Elapsed Time