RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.GsxUka/RM_769845.WedSep101437422025
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: 1757540261
Database = /dev/shm/rModeler.GsxUka/GCA_018154905.1_ASM1815490v1 
  - Sequences = 931
  - Bases = 19792732
  - N50 = 381743
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1057019-1132507 |                                                   [ 1 ]
  981532-1057019  |                                                   [  ]
  906045-981532   |                                                   [ 1 ]
  830558-906045   |                                                   [ 1 ]
  755071-830558   |                                                   [  ]
  679584-755071   |                                                   [  ]
  604097-679584   |                                                   [ 3 ]
  528609-604096   |                                                   [ 4 ]
  453122-528609   |                                                   [ 4 ]
  377635-453122   |                                                   [ 3 ]
  302148-377635   |                                                   [ 4 ]
  226661-302148   |                                                   [ 8 ]
  151174-226661   |                                                   [ 9 ]
  75687-151174    |*                                                  [ 19 ]
  200-75687       |************************************************** [ 874 ]

Storage Throughput = excellent ( 1659.35 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19792598 bp ( 19785041 non ambiguous )
   - Num Contigs Represented = 931
   - 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.. : 27 raw families identified
   - RepeatScout: Running filtering stage.. 27 families remaining
   - RepeatScout: 00:00:27 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 25 families... 00:00:04 (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: 00:00:34 (hh:mm:ss) Elapsed Time : 23 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...
       505 repeats masked totaling 73886 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10019319 bp
       Num Contigs Represented = 530
       Non ambiguous bp:
             Initial: 10015285 bp
             After Masking: 9884407 bp
             Masked: 1.31 % 
 -- Input Database Coverage: 10019319 bp out of 19792732 bp ( 50.62 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 257403
Comparison Time: 00:05:37 (hh:mm:ss) Elapsed Time, 17890 HSPs Collected
Number of families returned by RECON: 1671
Round Time: 00:06:06 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 39792732


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39792732 bp
   - Sequence extraction : 00:00:01 (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...
       978 repeats masked totaling 106693 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9773199 bp
       Num Contigs Represented = 462
       Non ambiguous bp:
             Initial: 9769676 bp
             After Masking: 9607578 bp
             Masked: 1.66 % 
 -- Input Database Coverage: 19792518 bp out of 19792732 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 202566
Comparison Time: 00:05:15 (hh:mm:ss) Elapsed Time, 5767 HSPs Collected
Number of families returned by RECON: 1277
Round Time: 00:05:54 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.GsxUka/RM_769845.WedSep101437422025
# 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: 00:12:41 (hh:mm:ss) Elapsed Time