RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.wi5Mzx/RM_1858034.FriSep122038152025
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: 1757734694
Database = /data/tmp/rModeler.wi5Mzx/GCA_051397715.1_GA10_1 
  - Sequences = 202
  - Bases = 38508758
  - N50 = 607360
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1825512-1955871 |                                                   [ 1 ]
  1695154-1825512 |                                                   [  ]
  1564796-1695154 |                                                   [  ]
  1434438-1564796 |                                                   [ 1 ]
  1304080-1434438 |                                                   [  ]
  1173722-1304080 |                                                   [ 1 ]
  1043364-1173722 |                                                   [ 2 ]
  913006-1043364  |*                                                  [ 3 ]
  782648-913006   |*                                                  [ 3 ]
  652290-782648   |**                                                 [ 7 ]
  521932-652290   |***                                                [ 9 ]
  391574-521932   |****                                               [ 11 ]
  261216-391574   |******                                             [ 16 ]
  130858-261216   |******                                             [ 16 ]
  500-130858      |************************************************** [ 132 ]

Storage Throughput = good ( 813.07 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38508721 bp ( 38508405 non ambiguous )
   - Num Contigs Represented = 202
   - 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.. : 21 raw families identified
   - RepeatScout: Running filtering stage.. 20 families remaining
   - RepeatScout: 00:01:05 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 17 families... 00:00:15 (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: 00:01:29 (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 : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       164 repeats masked totaling 60504 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10022251 bp
       Num Contigs Represented = 104
       Non ambiguous bp:
             Initial: 10022176 bp
             After Masking: 9948019 bp
             Masked: 0.74 % 
 -- Input Database Coverage: 10022251 bp out of 38508758 bp ( 26.03 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 39340
Comparison Time: 00:06:03 (hh:mm:ss) Elapsed Time, 1712 HSPs Collected
Number of families returned by RECON: 729
Round Time: 00:06:46 (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 : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       610 repeats masked totaling 138318 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28486390 bp
       Num Contigs Represented = 177
       Non ambiguous bp:
             Initial: 28486149 bp
             After Masking: 28306568 bp
             Masked: 0.63 % 
 -- Input Database Coverage: 38508641 bp out of 38508758 bp ( 100.00 % )
Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 337431
Comparison Time: 00:26:10 (hh:mm:ss) Elapsed Time, 13385 HSPs Collected
Number of families returned by RECON: 3648
Round Time: 00:29:26 (hh:mm:ss) Elapsed Time : 5 families discovered.

RepeatScout/RECON discovery complete: 24 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.wi5Mzx/RM_1858034.FriSep122038152025
# 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: 00:00:20 (hh:mm:ss) Elapsed Time


Program Time: 00:38:01 (hh:mm:ss) Elapsed Time