RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.RQgpI7/RM_3255752.ThuSep111443592025
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: 1757627038
Database = /data/tmp/rModeler.RQgpI7/GCA_025767605.1_ASM2576760v1 
  - Sequences = 1262
  - Bases = 15608989
  - N50 = 34448
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  285425-305777 |                                                   [ 1 ]
  265073-285424 |                                                   [  ]
  244721-265072 |                                                   [ 1 ]
  224370-244721 |                                                   [ 1 ]
  204018-224369 |                                                   [  ]
  183666-204017 |                                                   [ 1 ]
  163314-183665 |                                                   [ 2 ]
  142963-163314 |                                                   [ 2 ]
  122611-142962 |                                                   [ 4 ]
  102259-122610 |                                                   [ 7 ]
  81907-102258  |                                                   [ 8 ]
  61556-81907   |                                                   [ 14 ]
  41204-61555   |**                                                 [ 42 ]
  20852-41203   |******                                             [ 138 ]
  501-20852     |************************************************** [ 1041 ]

Storage Throughput = fair ( 626.77 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 15608957 bp ( 14800661 non ambiguous )
   - Num Contigs Represented = 1262
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 27 raw families identified
   - RepeatScout: Running filtering stage.. 27 families remaining
   - RepeatScout: 00:02:01 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 27 families... 00:00:17 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 5 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:02:23 (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 : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       348 repeats masked totaling 157985 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10565428 bp
       Num Contigs Represented = 879
       Non ambiguous bp:
             Initial: 10013650 bp
             After Masking: 9782232 bp
             Masked: 2.31 % 
 -- Input Database Coverage: 10565428 bp out of 15608989 bp ( 67.69 % )
Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 450775
Comparison Time: 00:09:10 (hh:mm:ss) Elapsed Time, 6323 HSPs Collected
Number of families returned by RECON: 1501
Round Time: 00:09:44 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 35608989


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 35608989 bp
   - Sequence extraction : 00:00:00 (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...
       194 repeats masked totaling 66661 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 5043449 bp
       Num Contigs Represented = 436
       Non ambiguous bp:
             Initial: 4786931 bp
             After Masking: 4688305 bp
             Masked: 2.06 % 
 -- Input Database Coverage: 15608877 bp out of 15608989 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 102378
Comparison Time: 00:03:14 (hh:mm:ss) Elapsed Time, 1052 HSPs Collected
Number of families returned by RECON: 451
Round Time: 00:03:24 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 23 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.RQgpI7/RM_3255752.ThuSep111443592025
# 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: 00:15:38 (hh:mm:ss) Elapsed Time