RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.uUC5pz/RM_392719.ThuFeb121053392026
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: 1770922418
Database = /dev/shm/rModeler.uUC5pz/GCA_012184645.1_IPPP_Chae_K1.1 
  - Sequences = 350
  - Bases = 13207566
  - N50 = 78350
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  366708-392866 |                                                   [ 1 ]
  340551-366708 |                                                   [  ]
  314394-340551 |                                                   [  ]
  288237-314394 |                                                   [  ]
  262080-288237 |                                                   [  ]
  235923-262080 |                                                   [ 1 ]
  209766-235923 |                                                   [ 2 ]
  183608-209765 |                                                   [ 1 ]
  157451-183608 |*                                                  [ 6 ]
  131294-157451 |*                                                  [ 5 ]
  105137-131294 |***                                                [ 12 ]
  78980-105137  |*****                                              [ 22 ]
  52823-78980   |********                                           [ 34 ]
  26666-52823   |********************                               [ 77 ]
  509-26666     |************************************************** [ 189 ]

Storage Throughput = excellent ( 1684.73 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 13207491 bp ( 13207371 non ambiguous )
   - Num Contigs Represented = 350
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 14 raw families identified
   - RepeatScout: Running filtering stage.. 12 families remaining
   - RepeatScout: 00:00:16 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 9 families... 00:00:05 (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: 00:00:23 (hh:mm:ss) Elapsed Time : 8 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 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       177 repeats masked totaling 45966 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10007430 bp
       Num Contigs Represented = 273
       Non ambiguous bp:
             Initial: 10007330 bp
             After Masking: 9922420 bp
             Masked: 0.85 % 
 -- Input Database Coverage: 10007430 bp out of 13207566 bp ( 75.77 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 79401
Comparison Time: 00:03:59 (hh:mm:ss) Elapsed Time, 3316 HSPs Collected
Number of families returned by RECON: 910
Round Time: 00:04:11 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 33207566


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 33207566 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       60 repeats masked totaling 14068 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 3200025 bp
       Num Contigs Represented = 138
       Non ambiguous bp:
             Initial: 3200005 bp
             After Masking: 3178016 bp
             Masked: 0.69 % 
 -- Input Database Coverage: 13207455 bp out of 13207566 bp ( 100.00 % )
Sampling Time: 00:00:04 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 11935
Comparison Time: 00:01:07 (hh:mm:ss) Elapsed Time, 285 HSPs Collected
Number of families returned by RECON: 147
Round Time: 00:01:11 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 9 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.uUC5pz/RM_392719.ThuFeb121053392026
# 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: 00:00:05 (hh:mm:ss) Elapsed Time


Program Time: 00:05:50 (hh:mm:ss) Elapsed Time