RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.H5vX3o/RM_3723179.FriSep120432262025
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: 1757676745
Database = /dev/shm/rModeler.H5vX3o/GCA_035078395.1_MYCT-0825-2021 
  - Sequences = 366
  - Bases = 14745396
  - N50 = 109559
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  265181-284087 |                                                   [ 2 ]
  246275-265180 |                                                   [ 1 ]
  227370-246275 |                                                   [ 2 ]
  208464-227369 |                                                   [ 2 ]
  189559-208464 |                                                   [ 3 ]
  170653-189558 |                                                   [ 3 ]
  151748-170653 |                                                   [  ]
  132842-151747 |****                                               [ 17 ]
  113937-132842 |**                                                 [ 11 ]
  95031-113936  |****                                               [ 17 ]
  76126-95031   |****                                               [ 18 ]
  57220-76125   |****                                               [ 19 ]
  38315-57220   |*******                                            [ 28 ]
  19409-38314   |***********                                        [ 46 ]
  504-19409     |************************************************** [ 197 ]

Storage Throughput = excellent ( 1701.53 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14745319 bp ( 14742186 non ambiguous )
   - Num Contigs Represented = 366
   - 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.. : 52 raw families identified
   - RepeatScout: Running filtering stage.. 49 families remaining
   - RepeatScout: 00:01:02 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 41 families... 00:00:20 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 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 : 37 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...
       572 repeats masked totaling 232484 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10025908 bp
       Num Contigs Represented = 283
       Non ambiguous bp:
             Initial: 10023595 bp
             After Masking: 9660575 bp
             Masked: 3.62 % 
 -- Input Database Coverage: 10025908 bp out of 14745396 bp ( 67.99 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 87153
Comparison Time: 00:06:04 (hh:mm:ss) Elapsed Time, 3803 HSPs Collected
Number of families returned by RECON: 998
Round Time: 00:06:28 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 34745396


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34745396 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...
       282 repeats masked totaling 114484 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4719331 bp
       Num Contigs Represented = 150
       Non ambiguous bp:
             Initial: 4718511 bp
             After Masking: 4552260 bp
             Masked: 3.52 % 
 -- Input Database Coverage: 14745239 bp out of 14745396 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 19306
Comparison Time: 00:02:19 (hh:mm:ss) Elapsed Time, 983 HSPs Collected
Number of families returned by RECON: 310
Round Time: 00:02:28 (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.H5vX3o/RM_3723179.FriSep120432262025
# 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: 00:10:29 (hh:mm:ss) Elapsed Time