RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.ZfiUqR/RM_1117433.FriSep121947142025
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: 1757731634
Database = /dev/shm/rModeler.ZfiUqR/GCA_051397425.1_GA10_22 
  - Sequences = 243
  - Bases = 38609474
  - N50 = 717404
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2121772-2273292 |                                                   [ 1 ]
  1970253-2121772 |                                                   [  ]
  1818734-1970253 |                                                   [ 1 ]
  1667214-1818733 |                                                   [  ]
  1515695-1667214 |                                                   [ 1 ]
  1364176-1515695 |                                                   [  ]
  1212656-1364175 |                                                   [ 2 ]
  1061137-1212656 |                                                   [ 2 ]
  909618-1061137  |                                                   [ 3 ]
  758098-909617   |*                                                  [ 4 ]
  606579-758098   |**                                                 [ 10 ]
  455060-606579   |**                                                 [ 9 ]
  303540-455059   |**                                                 [ 8 ]
  152021-303540   |****                                               [ 15 ]
  502-152021      |************************************************** [ 187 ]

Storage Throughput = excellent ( 1650.70 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38609380 bp ( 38608995 non ambiguous )
   - Num Contigs Represented = 243
   - 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.. : 30 raw families identified
   - RepeatScout: Running filtering stage.. 25 families remaining
   - RepeatScout: 00:00:38 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 22 families... 00:00:09 (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: 00:00:52 (hh:mm:ss) Elapsed Time : 21 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       197 repeats masked totaling 48331 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10021566 bp
       Num Contigs Represented = 109
       Non ambiguous bp:
             Initial: 10021460 bp
             After Masking: 9957807 bp
             Masked: 0.64 % 
 -- Input Database Coverage: 10021566 bp out of 38609474 bp ( 25.96 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 43365
Comparison Time: 00:03:50 (hh:mm:ss) Elapsed Time, 1906 HSPs Collected
Number of families returned by RECON: 770
Round Time: 00:04:01 (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 : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       654 repeats masked totaling 190038 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28587771 bp
       Num Contigs Represented = 200
       Non ambiguous bp:
             Initial: 28587492 bp
             After Masking: 28354464 bp
             Masked: 0.82 % 
 -- Input Database Coverage: 38609337 bp out of 38609474 bp ( 100.00 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 365940
Comparison Time: 00:14:42 (hh:mm:ss) Elapsed Time, 13892 HSPs Collected
Number of families returned by RECON: 3647
Round Time: 00:15:17 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 32 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.ZfiUqR/RM_1117433.FriSep121947142025
# 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: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:20:18 (hh:mm:ss) Elapsed Time