RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.FY1ZE4/RM_4118360.WedSep101407092025
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: 1757538428
Database = /dev/shm/rModeler.FY1ZE4/GCA_018154295.1_ASM1815429v1 
  - Sequences = 393
  - Bases = 19546661
  - N50 = 488124
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1743601-1868130 |                                                   [ 1 ]
  1619072-1743600 |                                                   [  ]
  1494544-1619072 |                                                   [ 1 ]
  1370015-1494543 |                                                   [  ]
  1245486-1370014 |                                                   [  ]
  1120958-1245486 |                                                   [  ]
  996429-1120957  |                                                   [ 1 ]
  871900-996428   |                                                   [ 1 ]
  747372-871900   |                                                   [ 1 ]
  622843-747371   |                                                   [ 1 ]
  498314-622842   |                                                   [ 4 ]
  373786-498314   |                                                   [ 7 ]
  249257-373785   |*                                                  [ 12 ]
  124728-249256   |*                                                  [ 10 ]
  200-124728      |************************************************** [ 354 ]

Storage Throughput = excellent ( 1635.21 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19546555 bp ( 19541765 non ambiguous )
   - Num Contigs Represented = 393
   - 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.. : 28 raw families identified
   - RepeatScout: Running filtering stage.. 28 families remaining
   - RepeatScout: 00:00:28 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 26 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:35 (hh:mm:ss) Elapsed Time : 22 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...
       352 repeats masked totaling 66288 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10001854 bp
       Num Contigs Represented = 227
       Non ambiguous bp:
             Initial: 10000044 bp
             After Masking: 9873889 bp
             Masked: 1.26 % 
 -- Input Database Coverage: 10001854 bp out of 19546661 bp ( 51.17 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 93096
Comparison Time: 00:04:49 (hh:mm:ss) Elapsed Time, 19121 HSPs Collected
Number of families returned by RECON: 1639
Round Time: 00:05:20 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 39546661


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39546661 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...
       1866 repeats masked totaling 204313 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9544673 bp
       Num Contigs Represented = 215
       Non ambiguous bp:
             Initial: 9541693 bp
             After Masking: 9286088 bp
             Masked: 2.68 % 
 -- Input Database Coverage: 19546527 bp out of 19546661 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 81810
Comparison Time: 00:04:30 (hh:mm:ss) Elapsed Time, 2848 HSPs Collected
Number of families returned by RECON: 789
Round Time: 00:04:45 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.FY1ZE4/RM_4118360.WedSep101407092025
# 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: 00:10:45 (hh:mm:ss) Elapsed Time