RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.4E4OOE/RM_1709652.ThuFeb120559412026
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: 1770904780
Database = /dev/shm/rModeler.4E4OOE/GCA_030575055.1_ASM3057505v1 
  - Sequences = 188
  - Bases = 12618155
  - N50 = 140634
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  516688-553557 |                                                   [ 1 ]
  479819-516687 |                                                   [  ]
  442950-479818 |                                                   [ 1 ]
  406081-442949 |                                                   [  ]
  369212-406080 |                                                   [  ]
  332343-369211 |*                                                  [ 2 ]
  295474-332342 |                                                   [ 1 ]
  258605-295473 |                                                   [ 1 ]
  221736-258604 |**                                                 [ 5 ]
  184867-221735 |**                                                 [ 4 ]
  147998-184866 |*****                                              [ 9 ]
  111129-147997 |*******                                            [ 13 ]
  74260-111128  |************                                       [ 22 ]
  37391-74259   |*********************                              [ 39 ]
  523-37391     |************************************************** [ 90 ]

Storage Throughput = excellent ( 1637.34 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12618032 bp ( 12616132 non ambiguous )
   - Num Contigs Represented = 188
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 10 raw families identified
   - RepeatScout: Running filtering stage.. 10 families remaining
   - RepeatScout: 00:00:13 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 9 families... 00:00:05 (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: 00:00:20 (hh:mm:ss) Elapsed Time : 9 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...
       219 repeats masked totaling 34667 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10014248 bp
       Num Contigs Represented = 162
       Non ambiguous bp:
             Initial: 10012748 bp
             After Masking: 9945091 bp
             Masked: 0.68 % 
 -- Input Database Coverage: 10014248 bp out of 12618155 bp ( 79.36 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 56953
Comparison Time: 00:03:48 (hh:mm:ss) Elapsed Time, 3153 HSPs Collected
Number of families returned by RECON: 852
Round Time: 00:04:04 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 32618155


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32618155 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       94 repeats masked totaling 11244 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2603704 bp
       Num Contigs Represented = 70
       Non ambiguous bp:
             Initial: 2603304 bp
             After Masking: 2578706 bp
             Masked: 0.94 % 
 -- Input Database Coverage: 12617952 bp out of 12618155 bp ( 100.00 % )
Sampling Time: 00:00:03 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 4005
Comparison Time: 00:00:47 (hh:mm:ss) Elapsed Time, 209 HSPs Collected
Number of families returned by RECON: 114
Round Time: 00:00:50 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 11 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.4E4OOE/RM_1709652.ThuFeb120559412026
# 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: 00:05:19 (hh:mm:ss) Elapsed Time