RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.dBSS40/RM_41363.TueSep92240362025
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: 1757482835
Database = /dev/shm/rModeler.dBSS40/GCA_012182655.1_ASM1218265v1 
  - Sequences = 904
  - Bases = 22041311
  - N50 = 54046
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  190969-204574 |                                                   [ 1 ]
  177364-190968 |                                                   [ 4 ]
  163759-177363 |                                                   [ 3 ]
  150154-163758 |                                                   [ 2 ]
  136549-150153 |                                                   [ 8 ]
  122944-136548 |                                                   [ 4 ]
  109339-122943 |                                                   [ 10 ]
  95734-109338  |*                                                  [ 11 ]
  82129-95733   |*                                                  [ 18 ]
  68524-82128   |**                                                 [ 22 ]
  54919-68523   |***                                                [ 31 ]
  41314-54918   |******                                             [ 68 ]
  27709-41313   |*******                                            [ 78 ]
  14104-27708   |**************                                     [ 143 ]
  500-14104     |************************************************** [ 501 ]

Storage Throughput = excellent ( 1090.23 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22041286 bp ( 22029353 non ambiguous )
   - Num Contigs Represented = 904
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 6 raw families identified
   - RepeatScout: Running filtering stage.. 6 families remaining
   - RepeatScout: 00:00:41 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 6 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: 00:00:53 (hh:mm:ss) Elapsed Time : 5 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 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...
       57 repeats masked totaling 20365 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10013569 bp
       Num Contigs Represented = 467
       Non ambiguous bp:
             Initial: 10008335 bp
             After Masking: 9948766 bp
             Masked: 0.60 % 
 -- Input Database Coverage: 10013569 bp out of 22041311 bp ( 45.43 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 143380
Comparison Time: 00:07:28 (hh:mm:ss) Elapsed Time, 1238 HSPs Collected
Number of families returned by RECON: 616
Round Time: 00:07:54 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 42041311


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42041311 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       100 repeats masked totaling 41732 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 12027637 bp
       Num Contigs Represented = 551
       Non ambiguous bp:
             Initial: 12020938 bp
             After Masking: 11932349 bp
             Masked: 0.74 % 
 -- Input Database Coverage: 22041206 bp out of 22041311 bp ( 100.00 % )
Sampling Time: 00:00:23 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 214185
Comparison Time: 00:09:50 (hh:mm:ss) Elapsed Time, 2224 HSPs Collected
Number of families returned by RECON: 793
Round Time: 00:10:22 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 7 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.dBSS40/RM_41363.TueSep92240362025
# 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: 00:00:12 (hh:mm:ss) Elapsed Time


Program Time: 00:19:21 (hh:mm:ss) Elapsed Time