RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.gPJGj6/RM_2036767.FriSep120305292025
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: 1757671528
Database = /dev/shm/rModeler.gPJGj6/GCA_032356445.1_MYCT-0816-2021 
  - Sequences = 317
  - Bases = 14699323
  - N50 = 120167
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  253954-272058 |                                                   [ 3 ]
  235851-253954 |                                                   [ 3 ]
  217748-235851 |*                                                  [ 4 ]
  199644-217747 |                                                   [ 2 ]
  181541-199644 |*                                                  [ 4 ]
  163438-181541 |*                                                  [ 5 ]
  145335-163438 |**                                                 [ 8 ]
  127231-145334 |**                                                 [ 8 ]
  109128-127231 |***                                                [ 13 ]
  91025-109128  |***                                                [ 13 ]
  72922-91025   |***                                                [ 11 ]
  54818-72921   |*****                                              [ 19 ]
  36715-54818   |*********                                          [ 30 ]
  18612-36715   |*********                                          [ 31 ]
  509-18612     |************************************************** [ 163 ]

Storage Throughput = excellent ( 1602.74 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14699272 bp ( 14636711 non ambiguous )
   - Num Contigs Represented = 317
   - 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.. : 45 raw families identified
   - RepeatScout: Running filtering stage.. 41 families remaining
   - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 31 families... 00:00:16 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 6 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:22 (hh:mm:ss) Elapsed Time : 25 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       380 repeats masked totaling 193866 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10086703 bp
       Num Contigs Represented = 242
       Non ambiguous bp:
             Initial: 10024808 bp
             After Masking: 9730102 bp
             Masked: 2.94 % 
 -- Input Database Coverage: 10086703 bp out of 14699323 bp ( 68.62 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 74691
Comparison Time: 00:06:15 (hh:mm:ss) Elapsed Time, 3857 HSPs Collected
Number of families returned by RECON: 1022
Round Time: 00:06:33 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 34699323


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34699323 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...
       208 repeats masked totaling 107620 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4612489 bp
       Num Contigs Represented = 150
       Non ambiguous bp:
             Initial: 4611823 bp
             After Masking: 4438067 bp
             Masked: 3.77 % 
 -- Input Database Coverage: 14699192 bp out of 14699323 bp ( 100.00 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 18915
Comparison Time: 00:02:27 (hh:mm:ss) Elapsed Time, 1202 HSPs Collected
Number of families returned by RECON: 312
Round Time: 00:02:37 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.gPJGj6/RM_2036767.FriSep120305292025
# 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: 00:10:41 (hh:mm:ss) Elapsed Time