RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.Kdl1x9/RM_3523450.FriSep121936582025
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: 1757731017
Database = /dev/shm/rModeler.Kdl1x9/GCA_051397355.1_GA10_6-scaf.final.scaffolds.fasta 
  - Sequences = 232
  - Bases = 38499010
  - N50 = 531024
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1478661-1584244 |                                                   [ 1 ]
  1373078-1478660 |                                                   [  ]
  1267495-1373077 |                                                   [ 1 ]
  1161912-1267494 |                                                   [ 1 ]
  1056330-1161912 |                                                   [ 1 ]
  950747-1056329  |*                                                  [ 4 ]
  845164-950746   |                                                   [ 1 ]
  739581-845163   |                                                   [ 2 ]
  633998-739580   |*                                                  [ 4 ]
  528416-633998   |**                                                 [ 8 ]
  422833-528415   |**                                                 [ 6 ]
  317250-422832   |*****                                              [ 14 ]
  211667-317249   |*****                                              [ 15 ]
  106084-211666   |*************                                      [ 36 ]
  502-106084      |************************************************** [ 138 ]

Storage Throughput = excellent ( 1674.96 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38498864 bp ( 38497920 non ambiguous )
   - Num Contigs Represented = 232
   - 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.. : 23 raw families identified
   - RepeatScout: Running filtering stage.. 20 families remaining
   - RepeatScout: 00:00:37 (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 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       185 repeats masked totaling 59588 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10012573 bp
       Num Contigs Represented = 122
       Non ambiguous bp:
             Initial: 10012267 bp
             After Masking: 9937819 bp
             Masked: 0.74 % 
 -- Input Database Coverage: 10012573 bp out of 38499010 bp ( 26.01 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 43956
Comparison Time: 00:03:58 (hh:mm:ss) Elapsed Time, 1610 HSPs Collected
Number of families returned by RECON: 724
Round Time: 00:04:14 (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...
       584 repeats masked totaling 136701 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28486211 bp
       Num Contigs Represented = 203
       Non ambiguous bp:
             Initial: 28485573 bp
             After Masking: 28307902 bp
             Masked: 0.62 % 
 -- Input Database Coverage: 38498784 bp out of 38499010 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 335790
Comparison Time: 00:14:06 (hh:mm:ss) Elapsed Time, 14119 HSPs Collected
Number of families returned by RECON: 3496
Round Time: 00:14:41 (hh:mm:ss) Elapsed Time : 7 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.Kdl1x9/RM_3523450.FriSep121936582025
# 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: 00:19:50 (hh:mm:ss) Elapsed Time