RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.1txAPr/RM_14424.FriSep120339302025
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: 1757673569
Database = /dev/shm/rModeler.1txAPr/GCA_032356825.1_MYCT-0618-2021 
  - Sequences = 387
  - Bases = 14766694
  - N50 = 92547
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  290487-311200 |                                                   [ 1 ]
  269774-290486 |                                                   [ 1 ]
  249061-269773 |                                                   [  ]
  228348-249060 |                                                   [ 1 ]
  207635-228347 |                                                   [ 1 ]
  186922-207634 |                                                   [ 2 ]
  166209-186921 |*                                                  [ 7 ]
  145496-166208 |*                                                  [ 6 ]
  124783-145495 |*                                                  [ 8 ]
  104070-124782 |**                                                 [ 12 ]
  83357-104069  |******                                             [ 27 ]
  62644-83356   |*******                                            [ 29 ]
  41931-62643   |*****                                              [ 24 ]
  21218-41930   |***************                                    [ 63 ]
  506-21218     |************************************************** [ 205 ]

Storage Throughput = excellent ( 1639.34 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14766650 bp ( 14764800 non ambiguous )
   - Num Contigs Represented = 387
   - 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.. : 54 raw families identified
   - RepeatScout: Running filtering stage.. 48 families remaining
   - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 41 families... 00:00:15 (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: 00:01:21 (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 : 00:00:00 (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...
       529 repeats masked totaling 223600 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10021512 bp
       Num Contigs Represented = 294
       Non ambiguous bp:
             Initial: 10020242 bp
             After Masking: 9692387 bp
             Masked: 3.27 % 
 -- Input Database Coverage: 10021512 bp out of 14766694 bp ( 67.87 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 89676
Comparison Time: 00:06:30 (hh:mm:ss) Elapsed Time, 3728 HSPs Collected
Number of families returned by RECON: 988
Round Time: 00:06:57 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 34766694


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34766694 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...
       379 repeats masked totaling 132752 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4745058 bp
       Num Contigs Represented = 172
       Non ambiguous bp:
             Initial: 4744478 bp
             After Masking: 4550916 bp
             Masked: 4.08 % 
 -- Input Database Coverage: 14766570 bp out of 14766694 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 20706
Comparison Time: 00:02:20 (hh:mm:ss) Elapsed Time, 1069 HSPs Collected
Number of families returned by RECON: 321
Round Time: 00:02:29 (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: /dev/shm/rModeler.1txAPr/RM_14424.FriSep120339302025
# 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: 00:10:56 (hh:mm:ss) Elapsed Time