RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.KZy2ni/RM_1041535.FriSep120339562025
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: 1757673596
Database = /dev/shm/rModeler.KZy2ni/GCA_032356845.1_MYCT-0121-2021 
  - Sequences = 389
  - Bases = 14911904
  - N50 = 115530
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  255401-273609 |                                                   [ 1 ]
  237194-255401 |                                                   [ 2 ]
  218987-237194 |                                                   [ 2 ]
  200780-218987 |                                                   [ 3 ]
  182573-200780 |*                                                  [ 5 ]
  164365-182572 |                                                   [ 4 ]
  146158-164365 |*                                                  [ 5 ]
  127951-146158 |**                                                 [ 10 ]
  109744-127951 |***                                                [ 16 ]
  91537-109744  |***                                                [ 16 ]
  73329-91536   |***                                                [ 17 ]
  55122-73329   |****                                               [ 21 ]
  36915-55122   |****                                               [ 19 ]
  18708-36915   |********                                           [ 40 ]
  501-18708     |************************************************** [ 228 ]

Storage Throughput = excellent ( 1681.10 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14911812 bp ( 14909412 non ambiguous )
   - Num Contigs Represented = 389
   - 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.. : 69 raw families identified
   - RepeatScout: Running filtering stage.. 60 families remaining
   - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 54 families... 00:00:16 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 12 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:22 (hh:mm:ss) Elapsed Time : 42 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...
       641 repeats masked totaling 251473 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10002312 bp
       Num Contigs Represented = 304
       Non ambiguous bp:
             Initial: 10000492 bp
             After Masking: 9623977 bp
             Masked: 3.76 % 
 -- Input Database Coverage: 10002312 bp out of 14911904 bp ( 67.08 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 98346
Comparison Time: 00:06:39 (hh:mm:ss) Elapsed Time, 4115 HSPs Collected
Number of families returned by RECON: 1107
Round Time: 00:07:04 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 34911904


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34911904 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...
       321 repeats masked totaling 114703 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4909490 bp
       Num Contigs Represented = 158
       Non ambiguous bp:
             Initial: 4908910 bp
             After Masking: 4736116 bp
             Masked: 3.52 % 
 -- Input Database Coverage: 14911802 bp out of 14911904 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 20910
Comparison Time: 00:02:27 (hh:mm:ss) Elapsed Time, 698 HSPs Collected
Number of families returned by RECON: 304
Round Time: 00:02:36 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 43 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.KZy2ni/RM_1041535.FriSep120339562025
# 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: 00:11:10 (hh:mm:ss) Elapsed Time