RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.D1WXEb/RM_431220.WedSep101409252025
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: 1757538565
Database = /dev/shm/rModeler.D1WXEb/GCA_018153985.1_ASM1815398v1 
  - Sequences = 478
  - Bases = 19603521
  - N50 = 379914
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1742962-1867446 |                                                   [ 1 ]
  1618479-1742962 |                                                   [  ]
  1493996-1618479 |                                                   [  ]
  1369513-1493996 |                                                   [  ]
  1245030-1369513 |                                                   [  ]
  1120547-1245030 |                                                   [ 2 ]
  996064-1120547  |                                                   [  ]
  871581-996064   |                                                   [ 1 ]
  747098-871581   |                                                   [  ]
  622615-747098   |                                                   [ 1 ]
  498132-622615   |                                                   [ 1 ]
  373649-498132   |*                                                  [ 9 ]
  249166-373649   |*                                                  [ 14 ]
  124683-249166   |*                                                  [ 16 ]
  200-124683      |************************************************** [ 433 ]

Storage Throughput = excellent ( 1677.79 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19603409 bp ( 19599363 non ambiguous )
   - Num Contigs Represented = 478
   - 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.. : 29 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... 00:00:05 (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: 00:00:35 (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...
       389 repeats masked totaling 61372 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10020138 bp
       Num Contigs Represented = 292
       Non ambiguous bp:
             Initial: 10017883 bp
             After Masking: 9896830 bp
             Masked: 1.21 % 
 -- Input Database Coverage: 10020138 bp out of 19603521 bp ( 51.11 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 119805
Comparison Time: 00:04:52 (hh:mm:ss) Elapsed Time, 17096 HSPs Collected
Number of families returned by RECON: 1505
Round Time: 00:05:21 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 39603521


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39603521 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...
       2509 repeats masked totaling 274301 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9583269 bp
       Num Contigs Represented = 246
       Non ambiguous bp:
             Initial: 9581478 bp
             After Masking: 9254865 bp
             Masked: 3.41 % 
 -- Input Database Coverage: 19603407 bp out of 19603521 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 93528
Comparison Time: 00:04:39 (hh:mm:ss) Elapsed Time, 3015 HSPs Collected
Number of families returned by RECON: 787
Round Time: 00:04:55 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.D1WXEb/RM_431220.WedSep101409252025
# 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: 00:10:56 (hh:mm:ss) Elapsed Time