RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.ZMAtuL/RM_1537253.FriSep120428402025
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: 1757676520
Database = /dev/shm/rModeler.ZMAtuL/GCA_035078345.1_MYCT-1862-2021 
  - Sequences = 374
  - Bases = 14997229
  - N50 = 88253
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  600767-643643 |                                                   [ 1 ]
  557891-600766 |                                                   [  ]
  515015-557890 |                                                   [  ]
  472139-515014 |                                                   [  ]
  429263-472138 |                                                   [  ]
  386387-429262 |                                                   [  ]
  343511-386386 |                                                   [  ]
  300635-343510 |                                                   [  ]
  257759-300634 |                                                   [  ]
  214883-257758 |                                                   [ 1 ]
  172007-214882 |*                                                  [ 7 ]
  129131-172006 |**                                                 [ 15 ]
  86255-129130  |******                                             [ 34 ]
  43379-86254   |************                                       [ 63 ]
  504-43379     |************************************************** [ 253 ]

Storage Throughput = excellent ( 1445.66 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14997159 bp ( 14738094 non ambiguous )
   - Num Contigs Represented = 374
   - 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.. 45 families remaining
   - RepeatScout: 00:01:04 (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), 3 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:01:27 (hh:mm:ss) Elapsed Time : 31 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       475 repeats masked totaling 175692 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10119287 bp
       Num Contigs Represented = 293
       Non ambiguous bp:
             Initial: 10037704 bp
             After Masking: 9742206 bp
             Masked: 2.94 % 
 -- Input Database Coverage: 10119287 bp out of 14997229 bp ( 67.47 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 89253
Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 4049 HSPs Collected
Number of families returned by RECON: 1016
Round Time: 00:06:31 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 34997229


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34997229 bp
   - Sequence extraction : 00:00:00 (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...
       275 repeats masked totaling 126542 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4877839 bp
       Num Contigs Represented = 161
       Non ambiguous bp:
             Initial: 4700357 bp
             After Masking: 4535888 bp
             Masked: 3.50 % 
 -- Input Database Coverage: 14997126 bp out of 14997229 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 18915
Comparison Time: 00:02:22 (hh:mm:ss) Elapsed Time, 937 HSPs Collected
Number of families returned by RECON: 340
Round Time: 00:02:31 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 32 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.ZMAtuL/RM_1537253.FriSep120428402025
# 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: 00:10:36 (hh:mm:ss) Elapsed Time