RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.1mha7S/RM_411814.FriSep122006322025
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: 1757732792
Database = /data/tmp/rModeler.1mha7S/GCA_051397575.1_GA10_21 
  - Sequences = 190
  - Bases = 38452296
  - N50 = 810239
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2438249-2612374 |                                                   [ 2 ]
  2264125-2438249 |                                                   [  ]
  2090000-2264124 |                                                   [  ]
  1915876-2090000 |                                                   [ 1 ]
  1741751-1915875 |                                                   [  ]
  1567627-1741751 |                                                   [ 1 ]
  1393502-1567626 |                                                   [  ]
  1219378-1393502 |                                                   [ 2 ]
  1045253-1219377 |                                                   [ 2 ]
  871129-1045253  |*                                                  [ 4 ]
  697004-871128   |*                                                  [ 5 ]
  522880-697004   |**                                                 [ 6 ]
  348755-522879   |****                                               [ 13 ]
  174631-348755   |******                                             [ 18 ]
  507-174631      |*************************************************  [ 136 ]

Storage Throughput = excellent ( 1316.94 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38452148 bp ( 38451951 non ambiguous )
   - Num Contigs Represented = 190
   - 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.. : 21 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 17 families... 00:00:06 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 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 : 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       200 repeats masked totaling 39939 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10026120 bp
       Num Contigs Represented = 102
       Non ambiguous bp:
             Initial: 10026070 bp
             After Masking: 9972705 bp
             Masked: 0.53 % 
 -- Input Database Coverage: 10026120 bp out of 38452296 bp ( 26.07 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 41616
Comparison Time: 00:04:45 (hh:mm:ss) Elapsed Time, 1683 HSPs Collected
Number of families returned by RECON: 722
Round Time: 00:04:57 (hh:mm:ss) Elapsed Time : 0 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 00:00:18 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       485 repeats masked totaling 124216 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28425969 bp
       Num Contigs Represented = 157
       Non ambiguous bp:
             Initial: 28425822 bp
             After Masking: 28260689 bp
             Masked: 0.58 % 
 -- Input Database Coverage: 38452089 bp out of 38452296 bp ( 100.00 % )
Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 326028
Comparison Time: 00:18:05 (hh:mm:ss) Elapsed Time, 13905 HSPs Collected
Number of families returned by RECON: 3645
Round Time: 00:18:52 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.1mha7S/RM_411814.FriSep122006322025
# 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: 00:24:45 (hh:mm:ss) Elapsed Time