RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.d9eAzs/RM_1652332.TueSep90418062025
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: 1757416685
Database = /data/tmp/rModeler.d9eAzs/GCA_004307925.1_Dicsqu18370_1 
  - Sequences = 439
  - Bases = 39319619
  - N50 = 274707
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1456200-1560142 |                                                   [ 1 ]
  1352258-1456199 |                                                   [  ]
  1248316-1352257 |                                                   [ 1 ]
  1144374-1248315 |                                                   [  ]
  1040433-1144374 |                                                   [ 2 ]
  936491-1040432  |                                                   [  ]
  832549-936490   |                                                   [ 1 ]
  728607-832548   |                                                   [ 1 ]
  624665-728606   |                                                   [ 2 ]
  520724-624665   |                                                   [ 4 ]
  416782-520723   |                                                   [ 3 ]
  312840-416781   |**                                                 [ 14 ]
  208898-312839   |***                                                [ 21 ]
  104956-208897   |*********                                          [ 61 ]
  1015-104956     |************************************************** [ 328 ]

Storage Throughput = excellent ( 1572.85 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39319484 bp ( 38311988 non ambiguous )
   - Num Contigs Represented = 439
   - 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.. : 240 raw families identified
   - RepeatScout: Running filtering stage.. 237 families remaining
   - RepeatScout: 00:01:15 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 232 families... 00:00:41 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 48 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:02:03 (hh:mm:ss) Elapsed Time : 183 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 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2136 repeats masked totaling 771363 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10332890 bp
       Num Contigs Represented = 201
       Non ambiguous bp:
             Initial: 10033106 bp
             After Masking: 9255401 bp
             Masked: 7.75 % 
 -- Input Database Coverage: 10332890 bp out of 39319619 bp ( 26.28 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 58653
Comparison Time: 00:06:08 (hh:mm:ss) Elapsed Time, 3816 HSPs Collected
Number of families returned by RECON: 968
Round Time: 00:06:36 (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 00:00:24 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6006 repeats masked totaling 2158501 bp(s).
   - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28986523 bp
       Num Contigs Represented = 361
       Non ambiguous bp:
             Initial: 28278811 bp
             After Masking: 26102484 bp
             Masked: 7.70 % 
 -- Input Database Coverage: 39319413 bp out of 39319619 bp ( 100.00 % )
Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 428275
Comparison Time: 00:23:12 (hh:mm:ss) Elapsed Time, 22810 HSPs Collected
Number of families returned by RECON: 3741
Round Time: 00:25:49 (hh:mm:ss) Elapsed Time : 25 families discovered.

RepeatScout/RECON discovery complete: 210 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.d9eAzs/RM_1652332.TueSep90418062025
# 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: 00:00:43 (hh:mm:ss) Elapsed Time


Program Time: 00:35:11 (hh:mm:ss) Elapsed Time