RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.mgRH5o/RM_4187460.ThuSep110255092025
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: 1757584508
Database = /dev/shm/rModeler.mgRH5o/GCA_023079195.1_ASM2307919v1 
  - Sequences = 364
  - Bases = 39224885
  - N50 = 344494
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1585145-1698351 |                                                   [ 1 ]
  1471939-1585144 |                                                   [  ]
  1358734-1471939 |                                                   [  ]
  1245528-1358733 |                                                   [  ]
  1132323-1245528 |                                                   [ 1 ]
  1019117-1132322 |                                                   [ 1 ]
  905911-1019116  |                                                   [ 1 ]
  792706-905911   |                                                   [  ]
  679500-792705   |                                                   [ 3 ]
  566295-679500   |                                                   [ 3 ]
  453089-566294   |**                                                 [ 13 ]
  339883-453088   |*                                                  [ 10 ]
  226678-339883   |****                                               [ 24 ]
  113472-226677   |********                                           [ 45 ]
  267-113472      |************************************************** [ 262 ]

Storage Throughput = excellent ( 1638.89 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39224792 bp ( 39124276 non ambiguous )
   - Num Contigs Represented = 364
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 122 raw families identified
   - RepeatScout: Running filtering stage.. 119 families remaining
   - RepeatScout: 00:00:58 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 118 families... 00:01:30 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 21 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:02:34 (hh:mm:ss) Elapsed Time : 97 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...
       2143 repeats masked totaling 892486 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10049906 bp
       Num Contigs Represented = 167
       Non ambiguous bp:
             Initial: 10023510 bp
             After Masking: 9062234 bp
             Masked: 9.59 % 
 -- Input Database Coverage: 10049906 bp out of 39224885 bp ( 25.62 % )
Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 49770
Comparison Time: 00:04:01 (hh:mm:ss) Elapsed Time, 3814 HSPs Collected
Number of families returned by RECON: 663
Round Time: 00:04:21 (hh:mm:ss) Elapsed Time : 3 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6788 repeats masked totaling 2499616 bp(s).
   - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29174858 bp
       Num Contigs Represented = 306
       Non ambiguous bp:
             Initial: 29100738 bp
             After Masking: 26411934 bp
             Masked: 9.24 % 
 -- Input Database Coverage: 39224764 bp out of 39224885 bp ( 100.00 % )
Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 420903
Comparison Time: 00:15:37 (hh:mm:ss) Elapsed Time, 13780 HSPs Collected
Number of families returned by RECON: 2812
Round Time: 00:16:32 (hh:mm:ss) Elapsed Time : 22 families discovered.

RepeatScout/RECON discovery complete: 122 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.mgRH5o/RM_4187460.ThuSep110255092025
# 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: 00:00:23 (hh:mm:ss) Elapsed Time


Program Time: 00:23:50 (hh:mm:ss) Elapsed Time