RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.0XMSNl/RM_4178943.TueSep92221292025
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: 1757481689
Database = /dev/shm/rModeler.0XMSNl/GCA_012182645.1_ASM1218264v1 
  - Sequences = 824
  - Bases = 22057945
  - N50 = 58340
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  220779-236514 |                                                   [ 1 ]
  205045-220779 |                                                   [ 1 ]
  189311-205045 |                                                   [  ]
  173576-189310 |                                                   [ 5 ]
  157842-173576 |                                                   [ 5 ]
  142108-157842 |                                                   [ 4 ]
  126374-142108 |*                                                  [ 9 ]
  110639-126373 |                                                   [ 6 ]
  94905-110639  |*                                                  [ 17 ]
  79171-94905   |**                                                 [ 21 ]
  63437-79171   |**                                                 [ 26 ]
  47702-63436   |****                                               [ 42 ]
  31968-47702   |**********                                         [ 88 ]
  16234-31968   |******************                                 [ 162 ]
  500-16234     |************************************************** [ 437 ]

Storage Throughput = excellent ( 1049.03 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22057923 bp ( 22046648 non ambiguous )
   - Num Contigs Represented = 824
   - 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 5 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:52 (hh:mm:ss) Elapsed Time : 3 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       57 repeats masked totaling 12767 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10026730 bp
       Num Contigs Represented = 448
       Non ambiguous bp:
             Initial: 10021421 bp
             After Masking: 9966838 bp
             Masked: 0.54 % 
 -- Input Database Coverage: 10026730 bp out of 22057945 bp ( 45.46 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 133903
Comparison Time: 00:07:27 (hh:mm:ss) Elapsed Time, 1433 HSPs Collected
Number of families returned by RECON: 604
Round Time: 00:07:59 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 42057945


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42057945 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...
       137 repeats masked totaling 27905 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 12031135 bp
       Num Contigs Represented = 487
       Non ambiguous bp:
             Initial: 12025169 bp
             After Masking: 11951520 bp
             Masked: 0.61 % 
 -- Input Database Coverage: 22057865 bp out of 22057945 bp ( 100.00 % )
Sampling Time: 00:00:23 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 176121
Comparison Time: 00:09:25 (hh:mm:ss) Elapsed Time, 2115 HSPs Collected
Number of families returned by RECON: 824
Round Time: 00:09:59 (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.0XMSNl/RM_4178943.TueSep92221292025
# 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: 00:00:10 (hh:mm:ss) Elapsed Time


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