RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.Wamgwb/RM_1463643.ThuSep110553132025
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: 1757595193
Database = /dev/shm/rModeler.Wamgwb/GCA_023623415.1_ASM2362341v1 
  - Sequences = 1141
  - Bases = 15731258
  - N50 = 59216
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  307562-329496 |                                                   [ 1 ]
  285629-307562 |                                                   [  ]
  263696-285629 |                                                   [  ]
  241763-263696 |                                                   [ 1 ]
  219830-241763 |                                                   [ 2 ]
  197897-219830 |                                                   [ 2 ]
  175964-197897 |                                                   [ 2 ]
  154031-175964 |                                                   [ 2 ]
  132098-154031 |                                                   [ 6 ]
  110165-132098 |                                                   [ 6 ]
  88232-110165  |                                                   [ 11 ]
  66299-88232   |*                                                  [ 22 ]
  44366-66299   |**                                                 [ 53 ]
  22433-44366   |****                                               [ 85 ]
  500-22433     |************************************************** [ 948 ]

Storage Throughput = excellent ( 1646.63 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 15731175 bp ( 14908710 non ambiguous )
   - Num Contigs Represented = 1141
   - 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.. : 29 raw families identified
   - RepeatScout: Running filtering stage.. 29 families remaining
   - RepeatScout: 00:01:06 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 27 families... 00:00:19 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:28 (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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       338 repeats masked totaling 145563 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10570124 bp
       Num Contigs Represented = 761
       Non ambiguous bp:
             Initial: 10005935 bp
             After Masking: 9784404 bp
             Masked: 2.21 % 
 -- Input Database Coverage: 10570124 bp out of 15731258 bp ( 67.19 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 368511
Comparison Time: 00:07:35 (hh:mm:ss) Elapsed Time, 5690 HSPs Collected
Number of families returned by RECON: 1479
Round Time: 00:08:01 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 35731258


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 35731258 bp
   - Sequence extraction : 00:00:00 (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...
       252 repeats masked totaling 85756 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 5161021 bp
       Num Contigs Represented = 457
       Non ambiguous bp:
             Initial: 4902745 bp
             After Masking: 4784118 bp
             Masked: 2.42 % 
 -- Input Database Coverage: 15731145 bp out of 15731258 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 117370
Comparison Time: 00:03:16 (hh:mm:ss) Elapsed Time, 1039 HSPs Collected
Number of families returned by RECON: 470
Round Time: 00:03:28 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.Wamgwb/RM_1463643.ThuSep110553132025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:13:03 (hh:mm:ss) Elapsed Time