RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.IjwnsL/RM_2265225.FriSep120322572025
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: 1757672576
Database = /dev/shm/rModeler.IjwnsL/GCA_032356665.1_MYCT-1956-2021 
  - Sequences = 327
  - Bases = 14763713
  - N50 = 110339
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  335227-359137 |                                                   [ 2 ]
  311318-335227 |                                                   [ 1 ]
  287409-311318 |                                                   [  ]
  263500-287409 |                                                   [ 2 ]
  239591-263500 |                                                   [  ]
  215682-239591 |                                                   [ 2 ]
  191773-215682 |*                                                  [ 4 ]
  167864-191773 |*                                                  [ 5 ]
  143955-167864 |*                                                  [ 5 ]
  120046-143955 |****                                               [ 16 ]
  96137-120046  |*****                                              [ 20 ]
  72228-96137   |*****                                              [ 18 ]
  48319-72228   |*********                                          [ 32 ]
  24410-48319   |*************                                      [ 48 ]
  501-24410     |************************************************** [ 172 ]

Storage Throughput = excellent ( 1502.74 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14763687 bp ( 14736579 non ambiguous )
   - Num Contigs Represented = 327
   - 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.. : 49 raw families identified
   - RepeatScout: Running filtering stage.. 43 families remaining
   - RepeatScout: 00:01:05 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 36 families... 00:00:20 (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: 00:01:28 (hh:mm:ss) Elapsed Time : 33 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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       598 repeats masked totaling 256733 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10060479 bp
       Num Contigs Represented = 253
       Non ambiguous bp:
             Initial: 10034254 bp
             After Masking: 9668723 bp
             Masked: 3.64 % 
 -- Input Database Coverage: 10060479 bp out of 14763713 bp ( 68.14 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 77421
Comparison Time: 00:05:55 (hh:mm:ss) Elapsed Time, 3329 HSPs Collected
Number of families returned by RECON: 966
Round Time: 00:06:15 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 34763713


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34763713 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...
       334 repeats masked totaling 132721 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4703128 bp
       Num Contigs Represented = 145
       Non ambiguous bp:
             Initial: 4702245 bp
             After Masking: 4517676 bp
             Masked: 3.93 % 
 -- Input Database Coverage: 14763607 bp out of 14763713 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 18915
Comparison Time: 00:02:16 (hh:mm:ss) Elapsed Time, 822 HSPs Collected
Number of families returned by RECON: 301
Round Time: 00:02:26 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 34 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.IjwnsL/RM_2265225.FriSep120322572025
# 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: 00:10:16 (hh:mm:ss) Elapsed Time