RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.ODisZn/RM_4189252.FriSep120335112025
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: 1757673310
Database = /dev/shm/rModeler.ODisZn/GCA_032356785.1_MYCT-1211-2021 
  - Sequences = 323
  - Bases = 14785093
  - N50 = 108939
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  310529-332674 |                                                   [ 2 ]
  288384-310528 |                                                   [  ]
  266239-288383 |                                                   [  ]
  244094-266238 |                                                   [ 2 ]
  221949-244093 |*                                                  [ 4 ]
  199804-221948 |                                                   [ 3 ]
  177659-199803 |*                                                  [ 5 ]
  155514-177658 |                                                   [ 2 ]
  133369-155513 |***                                                [ 11 ]
  111224-133368 |***                                                [ 11 ]
  89079-111223  |******                                             [ 22 ]
  66934-89078   |******                                             [ 22 ]
  44789-66933   |********                                           [ 28 ]
  22644-44788   |***************                                    [ 50 ]
  500-22644     |************************************************** [ 161 ]

Storage Throughput = excellent ( 1662.00 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14785043 bp ( 14775234 non ambiguous )
   - Num Contigs Represented = 323
   - 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.. 44 families remaining
   - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 34 families... 00:00:19 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:25 (hh:mm:ss) Elapsed Time : 32 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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       581 repeats masked totaling 255846 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10026798 bp
       Num Contigs Represented = 233
       Non ambiguous bp:
             Initial: 10017839 bp
             After Masking: 9648891 bp
             Masked: 3.68 % 
 -- Input Database Coverage: 10026798 bp out of 14785093 bp ( 67.82 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 71631
Comparison Time: 00:05:51 (hh:mm:ss) Elapsed Time, 3616 HSPs Collected
Number of families returned by RECON: 1004
Round Time: 00:06:28 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 34785093


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34785093 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...
       314 repeats masked totaling 114241 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4758165 bp
       Num Contigs Represented = 161
       Non ambiguous bp:
             Initial: 4757315 bp
             After Masking: 4590244 bp
             Masked: 3.51 % 
 -- Input Database Coverage: 14784963 bp out of 14785093 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 20910
Comparison Time: 00:02:32 (hh:mm:ss) Elapsed Time, 789 HSPs Collected
Number of families returned by RECON: 312
Round Time: 00:02:42 (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.ODisZn/RM_4189252.FriSep120335112025
# 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: 00:10:44 (hh:mm:ss) Elapsed Time