RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.w9hTnV/RM_2046494.FriSep120503442025
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: 1757678624
Database = /dev/shm/rModeler.w9hTnV/GCA_037041495.1_ASM3704149v1 
  - Sequences = 12625
  - Bases = 37908741
  - N50 = 6072
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  55439-59364 |                                                   [ 1 ]
  51515-55439 |                                                   [ 1 ]
  47591-51515 |                                                   [  ]
  43666-47590 |                                                   [ 2 ]
  39742-43666 |                                                   [ 1 ]
  35818-39742 |                                                   [ 5 ]
  31894-35818 |                                                   [ 8 ]
  27969-31893 |                                                   [ 15 ]
  24045-27969 |                                                   [ 39 ]
  20121-24045 |                                                   [ 67 ]
  16197-20121 |                                                   [ 137 ]
  12272-16196 |*                                                  [ 258 ]
  8348-12272  |**                                                 [ 559 ]
  4424-8348   |*****                                              [ 1168 ]
  500-4424    |************************************************** [ 10364 ]

  WARN: The N50 for this assembly is low ( <10,000 ).  The de novo methods
        employed by RepeatModeler are intended for use with long contiguous
        sequences and may not perform well with an over-abundance of short
        contigs in the database.
Storage Throughput = excellent ( 1626.49 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37908652 bp ( 37907136 non ambiguous )
   - Num Contigs Represented = 12625
   - 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.. : 222 raw families identified
   - RepeatScout: Running filtering stage.. 220 families remaining
   - RepeatScout: 00:01:22 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 210 families... 00:00:25 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 48 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:52 (hh:mm:ss) Elapsed Time : 162 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 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2648 repeats masked totaling 545371 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10001426 bp
       Num Contigs Represented = 3352
       Non ambiguous bp:
             Initial: 10001037 bp
             After Masking: 9436074 bp
             Masked: 5.65 % 
 -- Input Database Coverage: 10001426 bp out of 37908741 bp ( 26.38 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 5619628
Comparison Time: 00:14:18 (hh:mm:ss) Elapsed Time, 6323 HSPs Collected
Number of families returned by RECON: 2606
Round Time: 00:14:37 (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 00:00:18 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       7104 repeats masked totaling 1472068 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27907208 bp
       Num Contigs Represented = 9275
       Non ambiguous bp:
             Initial: 27906081 bp
             After Masking: 26374405 bp
             Masked: 5.49 % 
 -- Input Database Coverage: 37908634 bp out of 37908741 bp ( 100.00 % )
Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 43026726
Comparison Time: 00:45:27 (hh:mm:ss) Elapsed Time, 50360 HSPs Collected
Number of families returned by RECON: 9973
Round Time: 00:47:01 (hh:mm:ss) Elapsed Time : 16 families discovered.

RepeatScout/RECON discovery complete: 180 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.w9hTnV/RM_2046494.FriSep120503442025
# 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: 00:00:14 (hh:mm:ss) Elapsed Time


Program Time: 01:03:44 (hh:mm:ss) Elapsed Time