RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.QPf4rC/RM_3432668.MonSep81121142025
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: 1757355673
Database = /dev/shm/rModeler.QPf4rC/GCA_000599445.1_CS3005v1 
  - Sequences = 199
  - Bases = 36667552
  - N50 = 11267849
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  10516672-11267849 |                                                   [ 1 ]
  9765496-10516672  |                                                   [  ]
  9014319-9765495   |                                                   [  ]
  8263143-9014319   |                                                   [ 1 ]
  7511966-8263142   |                                                   [ 2 ]
  6760790-7511966   |                                                   [  ]
  6009613-6760789   |                                                   [  ]
  5258437-6009613   |                                                   [  ]
  4507260-5258436   |                                                   [  ]
  3756084-4507260   |                                                   [  ]
  3004907-3756083   |                                                   [  ]
  2253731-3004907   |                                                   [  ]
  1502554-2253730   |                                                   [  ]
  751378-1502554    |                                                   [  ]
  202-751378        |************************************************** [ 195 ]

Storage Throughput = excellent ( 1657.67 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36667446 bp ( 36593244 non ambiguous )
   - Num Contigs Represented = 199
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 24 raw families identified
   - RepeatScout: Running filtering stage.. 14 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 13 families... 00:00:21 (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: 00:01:05 (hh:mm:ss) Elapsed Time : 11 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 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       176 repeats masked totaling 37623 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10042518 bp
       Num Contigs Represented = 64
       Non ambiguous bp:
             Initial: 10022820 bp
             After Masking: 9976327 bp
             Masked: 0.46 % 
 -- Input Database Coverage: 10042518 bp out of 36667552 bp ( 27.39 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 47278
Comparison Time: 00:04:20 (hh:mm:ss) Elapsed Time, 35584 HSPs Collected
Number of families returned by RECON: 905
Round Time: 00:04:38 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       507 repeats masked totaling 94926 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26624848 bp
       Num Contigs Represented = 139
       Non ambiguous bp:
             Initial: 26570344 bp
             After Masking: 26441427 bp
             Masked: 0.49 % 
 -- Input Database Coverage: 36667366 bp out of 36667552 bp ( 100.00 % )
Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 316410
Comparison Time: 00:14:50 (hh:mm:ss) Elapsed Time, 170602 HSPs Collected
Number of families returned by RECON: 3379
Round Time: 01:39:53 (hh:mm:ss) Elapsed Time : 7 families discovered.

RepeatScout/RECON discovery complete: 20 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.QPf4rC/RM_3432668.MonSep81121142025
# 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: 00:00:14 (hh:mm:ss) Elapsed Time


Program Time: 01:45:50 (hh:mm:ss) Elapsed Time