RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.fwZG12/RM_2309144.FriSep120327292025
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: 1757672849
Database = /dev/shm/rModeler.fwZG12/GCA_032356745.1_MYCT-1733-2021 
  - Sequences = 379
  - Bases = 14770492
  - N50 = 96805
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  276721-296450 |                                                   [ 1 ]
  256992-276720 |                                                   [ 1 ]
  237263-256991 |                                                   [ 2 ]
  217534-237262 |                                                   [  ]
  197805-217533 |                                                   [ 2 ]
  178076-197804 |*                                                  [ 5 ]
  158347-178075 |*                                                  [ 6 ]
  138619-158347 |*                                                  [ 4 ]
  118890-138618 |**                                                 [ 10 ]
  99161-118889  |****                                               [ 16 ]
  79432-99160   |****                                               [ 18 ]
  59703-79431   |*******                                            [ 29 ]
  39974-59702   |*********                                          [ 37 ]
  20245-39973   |************                                       [ 49 ]
  517-20245     |************************************************** [ 199 ]

Storage Throughput = excellent ( 1642.47 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14770413 bp ( 14754210 non ambiguous )
   - Num Contigs Represented = 379
   - 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.. : 60 raw families identified
   - RepeatScout: Running filtering stage.. 55 families remaining
   - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 43 families... 00:00:35 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:41 (hh:mm:ss) Elapsed Time : 41 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...
       697 repeats masked totaling 260668 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10027501 bp
       Num Contigs Represented = 300
       Non ambiguous bp:
             Initial: 10011728 bp
             After Masking: 9618938 bp
             Masked: 3.92 % 
 -- Input Database Coverage: 10027501 bp out of 14770492 bp ( 67.89 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 97020
Comparison Time: 00:05:58 (hh:mm:ss) Elapsed Time, 4037 HSPs Collected
Number of families returned by RECON: 995
Round Time: 00:06:25 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 34770492


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34770492 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...
       376 repeats masked totaling 139679 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4742902 bp
       Num Contigs Represented = 164
       Non ambiguous bp:
             Initial: 4742472 bp
             After Masking: 4557256 bp
             Masked: 3.91 % 
 -- Input Database Coverage: 14770403 bp out of 14770492 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 17955
Comparison Time: 00:02:19 (hh:mm:ss) Elapsed Time, 674 HSPs Collected
Number of families returned by RECON: 325
Round Time: 00:02:37 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 44 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.fwZG12/RM_2309144.FriSep120327292025
# 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: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:10:51 (hh:mm:ss) Elapsed Time