RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.MhroSJ/RM_3028278.TueSep90407482025
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: 1757416068
Database = /dev/shm/rModeler.MhroSJ/GCA_004307915.1_Dicsqu463_1 
  - Sequences = 1259
  - Bases = 36868345
  - N50 = 75167
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  739905-792684 |                                                   [ 1 ]
  687126-739904 |                                                   [  ]
  634347-687125 |                                                   [  ]
  581568-634346 |                                                   [  ]
  528789-581567 |                                                   [  ]
  476010-528788 |                                                   [  ]
  423231-476009 |                                                   [  ]
  370453-423231 |                                                   [  ]
  317674-370452 |                                                   [ 2 ]
  264895-317673 |                                                   [ 5 ]
  212116-264894 |                                                   [ 8 ]
  159337-212115 |                                                   [ 15 ]
  106558-159336 |*                                                  [ 42 ]
  53779-106557  |*****                                              [ 123 ]
  1001-53779    |*************************************************  [ 1063 ]

Storage Throughput = excellent ( 1650.03 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36868279 bp ( 36778997 non ambiguous )
   - Num Contigs Represented = 1259
   - 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.. : 203 raw families identified
   - RepeatScout: Running filtering stage.. 202 families remaining
   - RepeatScout: 00:00:46 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 198 families... 00:00:27 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 29 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:01:18 (hh:mm:ss) Elapsed Time : 168 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...
       1832 repeats masked totaling 527667 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10032192 bp
       Num Contigs Represented = 423
       Non ambiguous bp:
             Initial: 10014249 bp
             After Masking: 9480987 bp
             Masked: 5.33 % 
 -- Input Database Coverage: 10032192 bp out of 36868345 bp ( 27.21 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 116886
Comparison Time: 00:04:51 (hh:mm:ss) Elapsed Time, 3250 HSPs Collected
Number of families returned by RECON: 963
Round Time: 00:05:18 (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 : 00:00:02 (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...
       4617 repeats masked totaling 1291513 bp(s).
   - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26836045 bp
       Num Contigs Represented = 981
       Non ambiguous bp:
             Initial: 26764706 bp
             After Masking: 25456175 bp
             Masked: 4.89 % 
 -- Input Database Coverage: 36868237 bp out of 36868345 bp ( 100.00 % )
Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 856086
Comparison Time: 00:17:14 (hh:mm:ss) Elapsed Time, 22403 HSPs Collected
Number of families returned by RECON: 3931
Round Time: 00:18:10 (hh:mm:ss) Elapsed Time : 22 families discovered.

RepeatScout/RECON discovery complete: 192 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.MhroSJ/RM_3028278.TueSep90407482025
# 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: 00:00:18 (hh:mm:ss) Elapsed Time


Program Time: 00:25:04 (hh:mm:ss) Elapsed Time