RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.ItPTca/RM_382463.ThuFeb121051382026
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: 1770922298
Database = /dev/shm/rModeler.ItPTca/GCA_012184655.1_IPPP_Chae_K2.1 
  - Sequences = 387
  - Bases = 13262133
  - N50 = 75241
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  234343-251044 |                                                   [ 1 ]
  217642-234342 |                                                   [  ]
  200941-217641 |                                                   [ 1 ]
  184241-200941 |                                                   [ 1 ]
  167540-184240 |*                                                  [ 6 ]
  150839-167539 |                                                   [ 3 ]
  134138-150838 |                                                   [ 3 ]
  117438-134138 |*                                                  [ 5 ]
  100737-117437 |***                                                [ 11 ]
  84036-100736  |***                                                [ 12 ]
  67335-84035   |******                                             [ 22 ]
  50635-67335   |******                                             [ 25 ]
  33934-50634   |***********                                        [ 41 ]
  17233-33933   |********************                               [ 75 ]
  533-17233     |************************************************** [ 181 ]

Storage Throughput = excellent ( 1683.52 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 13262055 bp ( 13261908 non ambiguous )
   - Num Contigs Represented = 387
   - 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.. : 11 raw families identified
   - RepeatScout: Running filtering stage.. 10 families remaining
   - RepeatScout: 00:00:17 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 7 families... 00:00:04 (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: 00:00:23 (hh:mm:ss) Elapsed Time : 7 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...
       165 repeats masked totaling 39537 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10026519 bp
       Num Contigs Represented = 316
       Non ambiguous bp:
             Initial: 10026382 bp
             After Masking: 9953985 bp
             Masked: 0.72 % 
 -- Input Database Coverage: 10026519 bp out of 13262133 bp ( 75.60 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 98346
Comparison Time: 00:04:10 (hh:mm:ss) Elapsed Time, 3564 HSPs Collected
Number of families returned by RECON: 921
Round Time: 00:04:32 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 33262133


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 33262133 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...
       121 repeats masked totaling 18860 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 3235489 bp
       Num Contigs Represented = 128
       Non ambiguous bp:
             Initial: 3235479 bp
             After Masking: 3204832 bp
             Masked: 0.95 % 
 -- Input Database Coverage: 13262008 bp out of 13262133 bp ( 100.00 % )
Sampling Time: 00:00:04 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 9730
Comparison Time: 00:01:06 (hh:mm:ss) Elapsed Time, 244 HSPs Collected
Number of families returned by RECON: 131
Round Time: 00:01:10 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 10 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.ItPTca/RM_382463.ThuFeb121051382026
# 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: 00:06:10 (hh:mm:ss) Elapsed Time