RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.QD2Ubi/RM_3558699.WedSep101956532025
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: 1757559412
Database = /dev/shm/rModeler.QD2Ubi/GCA_020137435.1_ASM2013743v1 
  - Sequences = 636
  - Bases = 36964375
  - N50 = 118919
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  385360-412849 |                                                   [ 2 ]
  357871-385359 |                                                   [  ]
  330382-357870 |                                                   [ 1 ]
  302893-330381 |                                                   [ 2 ]
  275405-302893 |*                                                  [ 6 ]
  247916-275404 |                                                   [ 1 ]
  220427-247915 |*                                                  [ 8 ]
  192938-220426 |*                                                  [ 11 ]
  165449-192937 |**                                                 [ 14 ]
  137961-165449 |****                                               [ 28 ]
  110472-137960 |******                                             [ 37 ]
  82983-110471  |*******                                            [ 42 ]
  55494-82982   |***************                                    [ 90 ]
  28005-55493   |*******************                                [ 110 ]
  517-28005     |************************************************** [ 284 ]

Storage Throughput = excellent ( 1608.32 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36964292 bp ( 36963846 non ambiguous )
   - Num Contigs Represented = 636
   - 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.. : 17 raw families identified
   - RepeatScout: Running filtering stage.. 17 families remaining
   - RepeatScout: 00:00:36 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 16 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:46 (hh:mm:ss) Elapsed Time : 15 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...
       561 repeats masked totaling 63943 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10025263 bp
       Num Contigs Represented = 286
       Non ambiguous bp:
             Initial: 10025235 bp
             After Masking: 9952557 bp
             Masked: 0.72 % 
 -- Input Database Coverage: 10025263 bp out of 36964375 bp ( 27.12 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 66430
Comparison Time: 00:04:21 (hh:mm:ss) Elapsed Time, 1319 HSPs Collected
Number of families returned by RECON: 600
Round Time: 00:04:33 (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 : 00:00:02 (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...
       1428 repeats masked totaling 166607 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26938979 bp
       Num Contigs Represented = 525
       Non ambiguous bp:
             Initial: 26938561 bp
             After Masking: 26750191 bp
             Masked: 0.70 % 
 -- Input Database Coverage: 36964242 bp out of 36964375 bp ( 100.00 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 442270
Comparison Time: 00:14:51 (hh:mm:ss) Elapsed Time, 9950 HSPs Collected
Number of families returned by RECON: 2765
Round Time: 00:15:25 (hh:mm:ss) Elapsed Time : 14 families discovered.

RepeatScout/RECON discovery complete: 30 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.QD2Ubi/RM_3558699.WedSep101956532025
# 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: 00:00:05 (hh:mm:ss) Elapsed Time


Program Time: 00:20:49 (hh:mm:ss) Elapsed Time