RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.R08Oza/RM_881129.FriSep122001452025
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: 1757732505
Database = /dev/shm/rModeler.R08Oza/GCA_051397515.1_GA1_7 
  - Sequences = 245
  - Bases = 38555328
  - N50 = 660349
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1500634-1607787 |                                                   [ 2 ]
  1393482-1500634 |                                                   [  ]
  1286330-1393482 |                                                   [ 1 ]
  1179178-1286330 |                                                   [ 3 ]
  1072026-1179178 |                                                   [  ]
  964874-1072026  |                                                   [ 2 ]
  857722-964874   |                                                   [ 3 ]
  750569-857721   |*                                                  [ 4 ]
  643417-750569   |*                                                  [ 5 ]
  536265-643417   |                                                   [ 3 ]
  429113-536265   |**                                                 [ 8 ]
  321961-429113   |***                                                [ 10 ]
  214809-321961   |****                                               [ 14 ]
  107657-214809   |*******                                            [ 24 ]
  505-107657      |************************************************** [ 166 ]

Storage Throughput = excellent ( 1760.02 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38555264 bp ( 38554851 non ambiguous )
   - Num Contigs Represented = 245
   - 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: 00:00:38 (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), 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 : 19 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...
       182 repeats masked totaling 28344 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10039496 bp
       Num Contigs Represented = 112
       Non ambiguous bp:
             Initial: 10039379 bp
             After Masking: 9997934 bp
             Masked: 0.41 % 
 -- Input Database Coverage: 10039496 bp out of 38555328 bp ( 26.04 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 42195
Comparison Time: 00:03:47 (hh:mm:ss) Elapsed Time, 1656 HSPs Collected
Number of families returned by RECON: 749
Round Time: 00:03:59 (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 : 00:00:01 (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...
       636 repeats masked totaling 90483 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28515745 bp
       Num Contigs Represented = 215
       Non ambiguous bp:
             Initial: 28515449 bp
             After Masking: 28380649 bp
             Masked: 0.47 % 
 -- Input Database Coverage: 38555241 bp out of 38555328 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 365085
Comparison Time: 00:14:54 (hh:mm:ss) Elapsed Time, 13419 HSPs Collected
Number of families returned by RECON: 3609
Round Time: 00:15:45 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 32 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.R08Oza/RM_881129.FriSep122001452025
# 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: 00:20:37 (hh:mm:ss) Elapsed Time