RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.qn2JXW/RM_2314065.MonSep81744092025
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: 1757378649
Database = /dev/shm/rModeler.qn2JXW/GCA_002222325.1_Cryp_neof_Tu259_1_V1 
  - Sequences = 120
  - Bases = 18573228
  - N50 = 808689
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1182116-1266480 |                                                   [ 1 ]
  1097753-1182116 |*                                                  [ 2 ]
  1013390-1097753 |                                                   [  ]
  929026-1013389  |                                                   [  ]
  844663-929026   |*                                                  [ 3 ]
  760300-844663   |**                                                 [ 5 ]
  675937-760300   |                                                   [ 1 ]
  591573-675936   |*                                                  [ 3 ]
  507210-591573   |                                                   [ 1 ]
  422847-507210   |                                                   [  ]
  338484-422847   |**                                                 [ 5 ]
  254120-338483   |**                                                 [ 4 ]
  169757-254120   |**                                                 [ 5 ]
  85394-169757    |***                                                [ 6 ]
  1031-85394      |************************************************** [ 84 ]

Storage Throughput = excellent ( 1697.03 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18573184 bp ( 18366198 non ambiguous )
   - Num Contigs Represented = 120
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 32 raw families identified
   - RepeatScout: Running filtering stage.. 32 families remaining
   - RepeatScout: 00:00:16 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 31 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 7 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:24 (hh:mm:ss) Elapsed Time : 24 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       412 repeats masked totaling 115217 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10129952 bp
       Num Contigs Represented = 82
       Non ambiguous bp:
             Initial: 10012022 bp
             After Masking: 9885881 bp
             Masked: 1.26 % 
 -- Input Database Coverage: 10129952 bp out of 18573228 bp ( 54.54 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 45753
Comparison Time: 00:04:00 (hh:mm:ss) Elapsed Time, 3242 HSPs Collected
Number of families returned by RECON: 753
Round Time: 00:04:21 (hh:mm:ss) Elapsed Time : 6 families discovered.
   - Increasing sample size to include end piece now = 38573228


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38573228 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       400 repeats masked totaling 108687 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8443169 bp
       Num Contigs Represented = 72
       Non ambiguous bp:
             Initial: 8354113 bp
             After Masking: 8237018 bp
             Masked: 1.40 % 
 -- Input Database Coverage: 18573121 bp out of 18573228 bp ( 100.00 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32385
Comparison Time: 00:03:14 (hh:mm:ss) Elapsed Time, 1472 HSPs Collected
Number of families returned by RECON: 513
Round Time: 00:03:25 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 31 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.qn2JXW/RM_2314065.MonSep81744092025
# 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: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:08:17 (hh:mm:ss) Elapsed Time