RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.eZnjWa/RM_3931322.WedSep101956392025
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: 1757559398
Database = /data/tmp/rModeler.eZnjWa/GCA_020137885.1_ASM2013788v1 
  - Sequences = 687
  - Bases = 37039702
  - N50 = 105728
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  337899-361999 |                                                   [ 3 ]
  313799-337898 |                                                   [ 3 ]
  289699-313798 |                                                   [ 4 ]
  265600-289699 |                                                   [ 2 ]
  241500-265599 |                                                   [ 3 ]
  217400-241499 |*                                                  [ 7 ]
  193300-217399 |*                                                  [ 11 ]
  169201-193300 |**                                                 [ 13 ]
  145101-169200 |**                                                 [ 16 ]
  121001-145100 |****                                               [ 27 ]
  96901-121000  |****                                               [ 29 ]
  72802-96901   |*********                                          [ 56 ]
  48702-72801   |*************                                      [ 81 ]
  24602-48701   |************************                           [ 141 ]
  503-24602     |************************************************** [ 291 ]

Storage Throughput = good ( 733.13 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37039593 bp ( 37038571 non ambiguous )
   - Num Contigs Represented = 687
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 19 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:50 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:07 (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: 00:01:05 (hh:mm:ss) Elapsed Time : 17 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 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       540 repeats masked totaling 62012 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10032447 bp
       Num Contigs Represented = 274
       Non ambiguous bp:
             Initial: 10032239 bp
             After Masking: 9961557 bp
             Masked: 0.70 % 
 -- Input Database Coverage: 10032447 bp out of 37039702 bp ( 27.09 % )
Sampling Time: 00:00:14 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 66430
Comparison Time: 00:05:44 (hh:mm:ss) Elapsed Time, 1234 HSPs Collected
Number of families returned by RECON: 571
Round Time: 00:06:04 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1528 repeats masked totaling 167002 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27007135 bp
       Num Contigs Represented = 561
       Non ambiguous bp:
             Initial: 27006321 bp
             After Masking: 26815302 bp
             Masked: 0.71 % 
 -- Input Database Coverage: 37039582 bp out of 37039702 bp ( 100.00 % )
Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 473851
Comparison Time: 00:21:07 (hh:mm:ss) Elapsed Time, 10116 HSPs Collected
Number of families returned by RECON: 2849
Round Time: 00:22:08 (hh:mm:ss) Elapsed Time : 13 families discovered.

RepeatScout/RECON discovery complete: 31 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.eZnjWa/RM_3931322.WedSep101956392025
# 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: 00:29:27 (hh:mm:ss) Elapsed Time