RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.f1JfJu/RM_3936105.FriSep120135282025
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: 1757666127
Database = /dev/shm/rModeler.f1JfJu/GCA_030573285.1_ASM3057328v1 
  - Sequences = 344
  - Bases = 14464074
  - N50 = 86896
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  301331-322817 |                                                   [ 1 ]
  279846-301331 |                                                   [  ]
  258361-279846 |                                                   [  ]
  236876-258361 |*                                                  [ 4 ]
  215391-236876 |                                                   [ 2 ]
  193905-215390 |*                                                  [ 6 ]
  172420-193905 |                                                   [  ]
  150935-172420 |*                                                  [ 5 ]
  129450-150935 |*                                                  [ 6 ]
  107965-129450 |**                                                 [ 9 ]
  86479-107964  |*****                                              [ 17 ]
  64994-86479   |********                                           [ 28 ]
  43509-64994   |*********                                          [ 33 ]
  22024-43509   |******************                                 [ 64 ]
  539-22024     |************************************************** [ 169 ]

Storage Throughput = excellent ( 1668.18 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14463976 bp ( 14455576 non ambiguous )
   - Num Contigs Represented = 344
   - 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.. : 13 raw families identified
   - RepeatScout: Running filtering stage.. 10 families remaining
   - RepeatScout: 00:00:24 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 10 families... 00:00:06 (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: 00:00:33 (hh:mm:ss) Elapsed Time : 7 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 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5626 repeats masked totaling 506123 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10007801 bp
       Num Contigs Represented = 266
       Non ambiguous bp:
             Initial: 10001901 bp
             After Masking: 9417527 bp
             Masked: 5.84 % 
 -- Input Database Coverage: 10007801 bp out of 14464074 bp ( 69.19 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 79003
Comparison Time: 00:04:37 (hh:mm:ss) Elapsed Time, 29239 HSPs Collected
Number of families returned by RECON: 1160
Round Time: 00:04:50 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 34464074


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34464074 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2409 repeats masked totaling 205997 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4456157 bp
       Num Contigs Represented = 148
       Non ambiguous bp:
             Initial: 4453657 bp
             After Masking: 4225641 bp
             Masked: 5.12 % 
 -- Input Database Coverage: 14463958 bp out of 14464074 bp ( 100.00 % )
Sampling Time: 00:00:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 17578
Comparison Time: 00:01:55 (hh:mm:ss) Elapsed Time, 4579 HSPs Collected
Number of families returned by RECON: 318
Round Time: 00:02:00 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 7 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.f1JfJu/RM_3936105.FriSep120135282025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:07:29 (hh:mm:ss) Elapsed Time