RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.qKIV4M/RM_3636651.WedSep102006192025
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: 1757559979
Database = /dev/shm/rModeler.qKIV4M/GCA_020137375.1_ASM2013737v1 
  - Sequences = 677
  - Bases = 36995121
  - N50 = 136896
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  659251-706305 |                                                   [ 1 ]
  612197-659250 |                                                   [ 1 ]
  565144-612197 |                                                   [  ]
  518090-565143 |                                                   [  ]
  471036-518089 |                                                   [  ]
  423983-471036 |                                                   [  ]
  376929-423982 |                                                   [ 2 ]
  329875-376928 |                                                   [ 3 ]
  282822-329875 |*                                                  [ 9 ]
  235768-282821 |*                                                  [ 13 ]
  188714-235767 |*                                                  [ 17 ]
  141661-188714 |***                                                [ 30 ]
  94607-141660  |*******                                            [ 65 ]
  47553-94606   |************                                       [ 105 ]
  500-47553     |************************************************** [ 431 ]

Storage Throughput = excellent ( 1615.30 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36994969 bp ( 36994206 non ambiguous )
   - Num Contigs Represented = 677
   - 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.. : 18 raw families identified
   - RepeatScout: Running filtering stage.. 18 families remaining
   - RepeatScout: 00:00:38 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 17 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:48 (hh:mm:ss) Elapsed Time : 13 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       410 repeats masked totaling 49941 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10029328 bp
       Num Contigs Represented = 272
       Non ambiguous bp:
             Initial: 10029143 bp
             After Masking: 9969833 bp
             Masked: 0.59 % 
 -- Input Database Coverage: 10029328 bp out of 36995121 bp ( 27.11 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 66430
Comparison Time: 00:04:17 (hh:mm:ss) Elapsed Time, 1729 HSPs Collected
Number of families returned by RECON: 557
Round Time: 00:04:31 (hh:mm:ss) Elapsed Time : 3 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 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1472 repeats masked totaling 168571 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26965561 bp
       Num Contigs Represented = 564
       Non ambiguous bp:
             Initial: 26964983 bp
             After Masking: 26776431 bp
             Masked: 0.70 % 
 -- Input Database Coverage: 36994889 bp out of 36995121 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 518671
Comparison Time: 00:15:06 (hh:mm:ss) Elapsed Time, 10114 HSPs Collected
Number of families returned by RECON: 2786
Round Time: 00:15:39 (hh:mm:ss) Elapsed Time : 13 families discovered.

RepeatScout/RECON discovery complete: 29 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.qKIV4M/RM_3636651.WedSep102006192025
# 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: 00:21:03 (hh:mm:ss) Elapsed Time