RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.NooToz/RM_135586.TueSep92316572025
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: 1757485016
Database = /dev/shm/rModeler.NooToz/GCA_012922635.1_ASM1292263v1 
  - Sequences = 136
  - Bases = 19428531
  - N50 = 508982
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1091443-1169331 |*                                                  [ 2 ]
  1013555-1091442 |                                                   [  ]
  935667-1013554  |                                                   [ 1 ]
  857780-935667   |                                                   [ 1 ]
  779892-857779   |*                                                  [ 2 ]
  702004-779891   |                                                   [ 1 ]
  624116-702003   |                                                   [ 1 ]
  546229-624116   |*                                                  [ 3 ]
  468341-546228   |*                                                  [ 3 ]
  390453-468340   |**                                                 [ 5 ]
  312565-390452   |***                                                [ 7 ]
  234678-312565   |*                                                  [ 3 ]
  156790-234677   |*                                                  [ 3 ]
  78902-156789    |*********                                          [ 16 ]
  1015-78902      |************************************************** [ 88 ]

Storage Throughput = excellent ( 1100.22 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19428379 bp ( 19425146 non ambiguous )
   - Num Contigs Represented = 136
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 15 raw families identified
   - RepeatScout: Running filtering stage.. 15 families remaining
   - RepeatScout: 00:00:25 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 15 families... 00:00:06 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:00:39 (hh:mm:ss) Elapsed Time : 12 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 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       184 repeats masked totaling 44976 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10008392 bp
       Num Contigs Represented = 93
       Non ambiguous bp:
             Initial: 10006650 bp
             After Masking: 9939737 bp
             Masked: 0.67 % 
 -- Input Database Coverage: 10008392 bp out of 19428531 bp ( 51.51 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 42486
Comparison Time: 00:05:58 (hh:mm:ss) Elapsed Time, 3434 HSPs Collected
Number of families returned by RECON: 496
Round Time: 00:06:32 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 39428531


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39428531 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       209 repeats masked totaling 49833 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9419907 bp
       Num Contigs Represented = 92
       Non ambiguous bp:
             Initial: 9418416 bp
             After Masking: 9347504 bp
             Masked: 0.75 % 
 -- Input Database Coverage: 19428299 bp out of 19428531 bp ( 100.00 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 39903
Comparison Time: 00:05:26 (hh:mm:ss) Elapsed Time, 3816 HSPs Collected
Number of families returned by RECON: 478
Round Time: 00:05:58 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 15 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.NooToz/RM_135586.TueSep92316572025
# 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: 00:00:11 (hh:mm:ss) Elapsed Time


Program Time: 00:13:20 (hh:mm:ss) Elapsed Time