RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.8cKdcM/RM_1721058.MonSep81143042025
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: 1757356984
Database = /data/tmp/rModeler.8cKdcM/GCA_000633855.1_ASM63385v1 
  - Sequences = 150
  - Bases = 15326821
  - N50 = 745199
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2219386-2377843 |                                                   [ 1 ]
  2060930-2219386 |                                                   [  ]
  1902474-2060930 |                                                   [  ]
  1744018-1902474 |                                                   [  ]
  1585562-1744018 |                                                   [ 1 ]
  1427106-1585562 |                                                   [  ]
  1268650-1427106 |                                                   [  ]
  1110193-1268649 |                                                   [ 1 ]
  951737-1110193  |                                                   [ 1 ]
  793281-951737   |                                                   [  ]
  634825-793281   |                                                   [ 2 ]
  476369-634825   |*                                                  [ 5 ]
  317913-476369   |**                                                 [ 7 ]
  159457-317913   |**                                                 [ 6 ]
  1001-159457     |************************************************** [ 126 ]

Storage Throughput = excellent ( 1463.87 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 15326736 bp ( 14979755 non ambiguous )
   - Num Contigs Represented = 150
   - 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.. : 61 raw families identified
   - RepeatScout: Running filtering stage.. 59 families remaining
   - RepeatScout: 00:01:53 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 43 families... 00:01:50 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 2 satellite(s), 6 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:03:47 (hh:mm:ss) Elapsed Time : 35 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 00:00:24 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       459 repeats masked totaling 200036 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10270062 bp
       Num Contigs Represented = 106
       Non ambiguous bp:
             Initial: 10035217 bp
             After Masking: 9737487 bp
             Masked: 2.97 % 
 -- Input Database Coverage: 10270062 bp out of 15326821 bp ( 67.01 % )
Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 55611
Comparison Time: 00:07:37 (hh:mm:ss) Elapsed Time, 3486 HSPs Collected
Number of families returned by RECON: 947
Round Time: 00:08:20 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 35326821


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 35326821 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       344 repeats masked totaling 115600 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 5056617 bp
       Num Contigs Represented = 72
       Non ambiguous bp:
             Initial: 4944538 bp
             After Masking: 4791005 bp
             Masked: 3.11 % 
 -- Input Database Coverage: 15326679 bp out of 15326821 bp ( 100.00 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 15051
Comparison Time: 00:03:17 (hh:mm:ss) Elapsed Time, 932 HSPs Collected
Number of families returned by RECON: 356
Round Time: 00:03:30 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 38 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.8cKdcM/RM_1721058.MonSep81143042025
# 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: 00:00:09 (hh:mm:ss) Elapsed Time


Program Time: 00:15:46 (hh:mm:ss) Elapsed Time