RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.wocrvM/RM_3271750.ThuSep110405582025
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: 1757588758
Database = /dev/shm/rModeler.wocrvM/GCA_023373895.1_ASM2337389v1 
  - Sequences = 366
  - Bases = 14566570
  - N50 = 89397
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  374999-401641 |                                                   [ 1 ]
  348358-374999 |                                                   [  ]
  321717-348358 |                                                   [  ]
  295075-321716 |                                                   [  ]
  268434-295075 |                                                   [ 1 ]
  241793-268434 |                                                   [ 1 ]
  215152-241793 |                                                   [ 1 ]
  188510-215151 |                                                   [ 1 ]
  161869-188510 |                                                   [ 3 ]
  135228-161869 |**                                                 [ 9 ]
  108587-135228 |***                                                [ 17 ]
  81945-108586  |******                                             [ 28 ]
  55304-81945   |*******                                            [ 32 ]
  28663-55304   |*************                                      [ 57 ]
  2022-28663    |************************************************** [ 215 ]

Storage Throughput = excellent ( 1661.07 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14566519 bp ( 14029540 non ambiguous )
   - Num Contigs Represented = 366
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 19 raw families identified
   - RepeatScout: Running filtering stage.. 18 families remaining
   - RepeatScout: 00:01:00 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:07 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:10 (hh:mm:ss) Elapsed Time : 16 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       262 repeats masked totaling 104634 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10385796 bp
       Num Contigs Represented = 285
       Non ambiguous bp:
             Initial: 10002635 bp
             After Masking: 9846955 bp
             Masked: 1.56 % 
 -- Input Database Coverage: 10385796 bp out of 14566570 bp ( 71.30 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 90525
Comparison Time: 00:06:23 (hh:mm:ss) Elapsed Time, 3156 HSPs Collected
Number of families returned by RECON: 923
Round Time: 00:06:49 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 34566570


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34566570 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...
       181 repeats masked totaling 39999 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4180704 bp
       Num Contigs Represented = 143
       Non ambiguous bp:
             Initial: 4026886 bp
             After Masking: 3964204 bp
             Masked: 1.56 % 
 -- Input Database Coverage: 14566500 bp out of 14566570 bp ( 100.00 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 15400
Comparison Time: 00:02:08 (hh:mm:ss) Elapsed Time, 595 HSPs Collected
Number of families returned by RECON: 233
Round Time: 00:02:16 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 17 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.wocrvM/RM_3271750.ThuSep110405582025
# 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: 00:10:20 (hh:mm:ss) Elapsed Time